Kaitano Tembo, who has been under immense pressure in recent weeks, named a second string team for the second-leg encounter despite his side trailing 1-0 on aggregate.
Youngsters Luke Le Roux and Dylan Stoffels both started, while experienced duo of Clayton Daniels and Aubrey Modiba were left on the bench by the Zimbabwean-born tactician.
SuperSport pressed Gor Mahia from the start as they searched for an early goal which would have unsettled the reigning Kenyan Premier League champions.
However, they were wasteful as Sipho Mbule placed his effort over the crossbar before Stoffels was denied by K’Ogalo goalkeeper Boniface Oluoch.
Le Roux then connected well with a cross from Onismor Bhasera, but the former’s effort was blocked by the Mahia defence.
SuperSport kept pushing and they were awarded a free-kick in a promising area, and their set-piece specialist Thabo Mnyamane stepped up to force Oluoch into a route save.
The last chance of the first half fell for Bernard Ondiek, but the Gor Mahia midfielder placed his attempt wide with the SuperSport defence badly exposed.
The score was 0-0 between SuperSport and Gor Mahia at the interval with the visitors leading 1-0 on aggregate. Matsatsantsa had dominated the first half, but they could not beat Oluoch.
The Kenya international continued to keep Matsatsantsa at bay in the early stages of the second half as he produced a fine save to deny Stoffels, who was looking to score his first goal for the Tshwane giants.
However, Oluoch was finally beaten when the visitors netted an own goal through Haron Shakava to hand SuperSport the advantage and the tie was at this stage locked at 1-1 on aggregate.
It was end-to-end stuff, and Matsatsantsa's lead only lasted for a minute as Gor Mahia levelled matters to make it 1-1 on the night through Francis Kahata, who beat keeper Reyaad Pieterse.
The goal did not dampen SuperSport players' spirits as Mnyamane fired past Oluoch with a good strike to give the home side a 2-1 lead on the night - making it 2-2 on aggregate with K'Ogalo set to go through to the next round on away-goal rule.
The momentum was with Tembo's men in the latter stages of the game with Mnyamane forcing Oluoch with a great save, and Darrel Smith was also denied by the former Tusker shot-stopper.
Mnyamane was just too unfortunate not to extend Matsatsantsa's lead when his effort hit the upright with Oluoch well-beaten and this proved to be the last chance of the game as Gor Mahia stood firm at back, and ultimately, the match ended 2-1 in favour of the hosts.
As a result, Gor Mahia advanced to the group stages after winning the tie on away-goal rule following a 2-2 draw on aggregate, while last year's runners-up SuperSport bowed out of the tournament.