NMMU, the former whipping boys in the competition scored a few upsets this season, but their first ever victory over Tuks proved to be the most important one as they edged NWU-Pukke on points difference.
Meanwhile, Pukke staged a gutsy fightback against the table-topping Maties in Stellenbosch, with two late tries from wing Luther Obi earning them two bonus points in their 37-34 defeat, but it was not enough to move them past the Madibaz.
The Maties had cruised to a comfortable 24-0 lead in front of their home crowd but Pukke refused to give in and came within a single conversion of making the semi-finals.
Earlier the University of Johannesburg (UJ) denied Shimlas victory when scrumhalf Vian van der Walt scored two late tries to salvage a dramatic 26-26 draw in Johannesburg.
The result means Shimlas, who were reduced to 13-men in the final stages, cannot qualify for the semi-finals.
Shimlas seemed to have the game in the bag with a commanding 26-5 lead with 25 minutes left in the match.
However, the Johannesburg-based side scored 21 points in 13 minutes to draw an engrossing match.
The victory ensured a third place on the final standings for UJ, setting up an all-north semi-final showdown with Tuks in Pretoria next week.
NMMU will travel to Stellenbosch to take on the unbeaten Maties in their coastal semi-final derby.
In Cape Town, 2011 champions the University of Cape Town held off a determined Wits side to secure their first win of the season which saw plenty of tries on the Green Mile.
Ikeys took a 42-0 lead into the half-time break, but Wits fought back admirably and pushed UCT right until the end, with the hosts eventually hanging on for an entertaining 50-40 win.
It was Wits’ first four-try bonus point of the season, and although they ended their campaign winless their second half display showed their characteristic fighting spirit.
In the Varsity Shield, CUT continued their unbeaten run with a comprehensive 36-12 victory over Fort Hare in Alice, and Peter de Villiers’ UWC side notched their first away win of the season, beating UKZN 36-13 in Pietermaritzburg.
The match between UWC and Fort Hare next week in Bellville is effectively a semi-final, with the outcome of that game set to decide who faced the table-topping CUT in the final.