The young UCT side went down to their Maties counterparts in the last minute by 22:26 in a tight affair after having held the lead for most of the game.
UCT scored with only three minutes played and went ahead, but Maties struck back to equalise.
Next came a penalty and then it was powerful backrow forward Josh Katzen whow went over to move the Ikeys clear 15:7. Maties scored just before the half and UCT took a narrow 15:14 lead into the break.
The game stayed tightly contested and UCT was up 22:19 with moments to play, when Maties struck for the final time with a converted try to clinch the win 22:26.
Kevin Foote is not a coach to be happy with a loss but he stated: "The big thing is for me is that I want the guys I have here to learn from these games – win or lose.
"We have a very young team here and I would love it if we could go on and produce some new Varsity Cup players from this squad… with those players being wiser for the experience too."
NWU Pukke, the Ikeys opening round opposition, beat NMMU by 28:22 in round two and are now getting ready to play take on Varsity Cup champions Tuks, who advanced to the final beating UJ by 39:34.
Day Two results – Wednesday, July 4:
17. UL Turfloop 10 Venda 7, Pool D (Field A)
18. Varsity College 19 FNB CUT 20, Pool B (Field B)
19. FNB UKZN 46 DUT 3, Pool B (Field C)
20. Cida City 0 Medunsa 69, Pool D (Field D)
21. Rhodes 23 NWU-Vaal 31, Pool C (Field A)
22. UJ Soweto 17 CA 13, Pool D (Field B)
23. FNB Maties 26 FNB UCT 22, Pool A (Field C)
24. MUT 8 NMMU-G 39, Pool C (Field D)
25. FNB UP-Tuks 39 FNB UJ 34, Pool A (Field A)
26. WS Buffalo 27 CPUT 16, Pool C (Field B)
27. FNB Shimlas 42 FNB Wits 17, Pool A (Field C)
28. Zululand 3 WSU Ibika 16, Pool C (Field D)
29. FNB NMMU 22 FNB NWU-Pukke 28, Pool A (Field A)
30. FNB UWC 35 FNB TUT 26, Pool B (Field B)
31. FNB Fort Hare 27 Namibia 13, Pool B (Field C)
32. WSU Mthata 16 NWU-Maf 11, Pool D (Field D)