Jamie Cureton's 94th minute goal secured all three points for the Robins against AFC Wimbledon at the Abbey Business Stadium.
The striker was on hand just before the final whistle to chip an effort over Ross Worner to secure victory for Cheltenham.
The game will also be remembered for some controversial refereeing decisions.
Wimbledon were awarded an indirect free-kick late in the second half as Scott Brown picked up Matt Richards' back pass, whilst at the other end the referee awarded a penalty to Yates' men, only to overturn his own decision minutes later. An incident that may not even be explained with a video replay.
Mark Yates had made two changes to the side that lost against Torquay last Saturday.
Fit again Troy Brown joined loan signing James Wilson in central defence as veteran defender Steve Elliott dropped to the bench and Jason Taylor rejoined the Robins starting eleven in place of Sido Jombati as Matt Richards moved to left-back in a shake-up of the Cheltenham Town defence.
Former AFC Wimbledon striker Byron Harrison started at the top of the pitch against his former club. The striker featured against the Dons for only the second time after a 10 minute substitute appearance at the Abbey Business Stadium in March.
Today's visitors stuck with the same side the convincingly beat Burton Albion last weekend. The Dons' showed they were no pushovers in that game. They came back from a goal down to win with three second half goals.
Cheltenham started the first half in an unconventional way. They were forced to change ends at the kick-off and attacked the Liberty Mutual Insurance Stand in the opening 45 minutes.
It was a mixed half as the Visitor's started brightly and the Robins were unable to contain Wimbledon's passing play.
On his 250th appearance, Scott Brown was called into action early, comfortably savings Midson's headed attempt on goal.
The Dons left back Callum Kenedy was causing plenty of problems. His cross previously found Midson's head and another was put behind by Troy Brown shortly after. From the resulting corner, the influential defender's bending cross dropped just wide of Scott Brown's upright.
Wimbledon had plenty of possession but were struggling to take advantage as the Robins initially struggled to keep pace with the visitors.
However, the midfield pressing of Taylor, Noble and Penn in the Dons half started to ease the pressure on the home back line.
Byron Harrison carried his good run of form into this game, the striker had the Robins fans agasp as he won a corner and got his head on the end of it, unfortunately his effort was off target.
20 minutes in and the Robins had grown into the game and were able to match the visitors passing play during positive spells of possession.
Terry Gornell was released on the left side of the box and outpaced Fuller to they byline. He attempted to cut the ball square to Taylor but was denied well by Worner.
After several decent phases of pressing build up, Worner was on hand again to deny Harrison. The former Dons striker linked up well with David Noble but his ambitious overhead kick was easy enough to deal with and Worner was able to clutch his strike out of the air.
The visitors showed their frustration at their lack of possession as the game progressed, Harry Pell firing well over into the visiting fans from long range.
Harrison continued to cause problems for his old employers around the box. He out-muscled Andy Frampton in the Dons box before snatching a strike across the face of goal.
The game had slowed as it drew to a close and Richards found himself in a crossing position. David Noble popped up in the box to connect with the cross but couldn't direct his header past the grasp of Worner.
Half Time: Cheltenham Town 0-0 AFC Wimbledon
Roles were reversed in the second half as Cheltenham emerged from the half-time break the more determined and Jermaine McGlashan was a man on a mission as the half began.
His crunching tackle on Alan Bennett
unleashed Harrison into the box. Unselfishly, he played McGlashan back into the game and Gornell was unable to connect with his shot-come-cross.
Moments later, McGlashan latched onto Lowe's long ball and was allowed to advance deep into Dons defence. His left footed shot was well denied by Worner diving to his right at full stretch.
Harrison carried his first half performance with him into the second, heading just over the bar from Matt Richards' free kick. Shortly after, he was fortunate to latch onto a looping ball in the box that had failed to be cleared but his hopeful effort trickled out of play for a throw-in.
Cheltenham' great pressing in the midfield was strong enough to prevent the Dons from playing their passing style of football but the visitors were strong in defence to deny the Robins.
Numerous corners for the home side failed to offer a clear cut opportunity, Gornell with his back to goal being allowed to turn but found his shot well blocked in a crowded penalty area.
Wimbledon's first effort of second half was a tame shot by substitute Chris Arthur that caused little concern to Scott Brown diving to his left and their chances were few and far between as Michael Smith was on hand to head wide from a corner.
The final 10 minutes bordered on farcical.
Errors within the Robins defence led to the referee indicating an indirect free-kick on the edge of the six-yard box as Scott Brown handled Matt Richards' passback.
The Robins packed the goalmouth in front of the LMI Stand as Chris Arthur was perfectly tee'd up to strike but was unable to fire his shot on target.
What happened next was almost beyond belief.
The fans were left confused as the referee indicated a penalty for the Robins as the game came to a close. He promptly turned his back on the aggrieved Wimbledon players who ferociously appealed against his decision.
The general concensus was the Terry Gornell had been pushed in the six-yard box but after plenty of heated discussion on the pitch, the referee changed his mind. Running to the edge of the Dons six-yard box, he signalled for a free kick to the visiting players.
What ensued was a barage of boos from the home support but greeted with numerous cheers from the visiting fans.
In an immediate reply at the other end, Harry Pell came close to earning all three points as his deflected shot bounced just wide of goal.
But the glory of the afternoon was to belong to the Robins.
Jamie Cureton's substitue appearance, returning from injury proved fruitful for Cheltenham. He latched onto Troy Brown's huge clearing header that the Dons defence failed to handle and was on hand to chip his shot over a desperate Ross Worner to snatch a deserved lead in the 94th minute.
There was just enough time for Sido Jombati to make a substitute appearance before the referee blew for full time.
Cheltenham Town 1-0 AFC Wimbledon
Cheltenham Town FC (4-4-2): S. Brown (GK); Lowe, T. Brown, Wilson, Richards; Penn (c), Taylor, Noble (Cureton '75), McGlashan (Jombati '90+4), Gornell, Harrison
Subs not used: Roberts (GK); Elliott, Jombati, Kotwica, Vincent, Deering.
FC Wimbledon (4-4-2): Worner (GK);FUller, Frampton, Bennett (c), Kennedy (Fenlon '79); Francomb (Porter '65), S. Moore, Pell, L. Moore; Smith, Midson (Arthur '65).
Subs not used: Sweeney, Seb Brown (GK), Weston, Fayers.
Referee: Mr. Darren Drysdale
Attendance: 3,032 (519 Visiting Fans)
Star Man: Troy Brown