Burton Francis kicked a penalty in injury time to down the Stormers in Bloemfontein.
The Cheetahs won 26-24 after trailing 15-7 at halftime.
The two teams met in a pre-season in Bloemfontein and the Cheetahs, courtesy of a last minute penalty, won by a point.
This time, when it mattered most, the Cheetahs were as desperate in refusing to be beaten, and they simply refused to go away.
The Stormers appeared to have the game won when they fed the scrum in the 80th minute, but they conceded a tighthead and the Cheetahs were awarded the scrum with the final set phase play of the game.
Thereafter the hosts advanced play 60 metres, kept the ball for more than 10 phases and won the penalty at the breakdown. Francis, who enjoyed his finest match for the Cheetahs, was brilliant in converting the penalty from an acute angle.
Stormers captain Jean de Villiers applauded the Cheetahs victory and said his side were beaten by a better team.
The win, the fifth in succession, was a franchise record for the Cheetahs.
Andries Bekker, the first Stormer to play 100 matches for the franchise, was outstanding in all aspects of the game, but on balance the Cheetahs played with greater composure. Both sides were desperate for the win and both played with desire and determination but it was the Cheetahs who had the momentum when it mattered most.
Francis kicked 16 points, including a fantastic drop goal, and his performance was deserving of the man of match award.
The Cheetahs bench provided excellent impact, especially in the front row, and their scrum turnover was the defining moment of the game.
Both sides scored two tries and both played with intent and enterprise. The match was physical, it was bruising and it was entertaining.
The pre-match view of many, myself included, was that there wouldn’t be more than a point or two in this game. And so it proved.
The Stormers showed the desperation of a side that had to win to keep alive their play-off aspirations but the Cheetahs were equal in desperation and simply defiant. The home team had added defensive nous to their attack and they played with the confidence of a team that has a winning habit.
The Stormers forwards, in the first half, had the edge and Bekker disrupted the Cheetahs lineout and denied the hosts an attacking platform.
Somehow the Cheetahs managed the disruption and also the loss of replacement scrumhalf Sarel Pretorius whose try-scoring impact was immediate.
Reserve winger Rayno Benjamin played scrumhalf for the last quarter and his Sevens experience ensured he produced an inspiring cameo.
Joe Pietersen was effective for the Stormers with his goalkicking but the visitors attack never threatened and the back three of Jaco Taute, Gio Aplon and Pietersen struggled as a unit in the first quarter.
Taute’s miserable season in Cape Town continued and he left the field with a serious knee injury which could end his Super Rugby year.
Juan de Jongh scored a brace for the Stormers, but the second should not have been awarded because of an offside infringement and it was poetic justice when Pretorius intercepted a Nic Groom kick to score.
There was very little between the two teams in performance, but one team currently knows how to win and the other is making a habit of losing. This was the Stormers fourth defeat in six starts and next weekend’s match at Newlands against the Sharks could define their season.
By Mark Keohane