Cape Town - Two late bonus points saw NWU-Pukke sneak into the FNB Varsity Cup presented by Steinhoff International semi-finals ahead of Maties on points difference.
Last year's beaten finalists will face table-toppers FNB UP-Tuks in Pretoria next week, while defending champions UCT will travel to Bloemfontein to take on the unbeaten UFS-Shimlas in the other semi-final.
Three-time champions Maties romped to a comprehensive 53-8 victory over winless CUT in Bloemfontein, but it was not enough in the end as they miss the play-offs for just the second time in the history of the competition.
Although NWU-Pukke went down 29-26 to UFS-Shimlas in Bloemfontein, two late tries saw them pick up two vital bonus points to knock Maties out on points difference.
UFS-Shimlas are the only team that have not lost this season, but they ended in second place to UP-Tuks who were far too strong for NMMU.
The Pretoria outfit outscored the Madibaz by five tries to one in Port Elizabeth to seal top spot ahead of UFS-Shimlas on points difference.
UFS-Shimlas will host their first-ever semifinal against UCT who battled to a tough 8-0 victory over UJ on a windy Green Mile in Cape Town to secure their spot in the play-offs.
Ikeys flank Jason Klaasen scored the only try of the match in a tight encounter, which saw UJ end the season in sixth place ahead of NMMU and CUT - who finished their debut season without a single log point.
In the Varsity Shield UWC kept their hopes of sneaking into the final alive with a comprehensive 58-8 victory over Fort Hare in Alice despite being reduced to 14 men for most of the game.
Wits secured a home final with a comfortable 50-5 victory over TUT who have not won a single game this season.
The Varsity Young Guns final will be a replay of last year's dramatic clash between UFS and UP-Tuks, although this year they will be playing in Bloemfontein instead of Pretoria.
The Pretoria side handed the NMMU Young Guns their first defeat of the season to deny the Eastern Cape side a place in the final on points difference.
In the Steinhoff Koshuisrugby Championship Steinhoff Vishuis lost to Steinhoff Patria but secured their place in the final with a bonus point, while CUT's Steinhoff Tigers easily beat NMMU's Steinhoff Stallions.