WSU had fought back from 23-6 down midway through the second half to draw level after 66 minutes. WSU captain Litha Nkula then missed two late penalty goal attempts to win it, with the game going into extra time.
Nkula was on target with a penalty goal in the first half of extra time but it was Nkutu who snatched victory for CPUT with a 99th-minute try. He was also named the FNB Player That Rocks for the final.
It took five minutes of this match for the defending champions to show off their attacking prowess as they faked a driving maul to send the pass out wide to wing Asisipho Malotana to score the first try of the final.
With CPUT hooker Siyasanga Ngubelanga in the sin bin, WSU All Blacks could only land two penalties via the boot of Nkula. Then Ameer Hendricks (lock) scored the Capetonians' second try to see then take a 15-6 lead at the break.
Feghon-Leigh Snyders added a brilliant try to his earlier points via the boot, and then snapped over a drop goal minutes later to put CPUT firmly in control.
WSU finally secured their first try just after the second strategy break when Sakhele Ngeno (wing) raced over and when CPUT lost Mputa to a yellow card in the 62nd minute, the All Blacks struck as Nkula slotted his third penalty before scrumhalf Eric Mcaphukana dotted down from a dominant 5m scrum, with Nkula's conversion levelling the scores.
After a disallowed try and Nkula's two late penalty misses, the final was forced into extra-time, when Nkutu's heroics ensured CPUT defend their title.
To add the the Capetonians' celebrations in Pretoria on Sunday evening, Sesona Macala (CPUT No 8) has won the 2021 FNB Varsity Shield Overall Player That Rocks award. He received the award after his team's dramatic final victory at Tuks Stadium.
Macala, who scored three tries during the tournament, saw off the challenge of WSU lock Hlomla Payi and TUT Vikings flyhalf Lusanda Xakwana in a public vote on the Varsity Cup's Facebook page.
Meanwhile, CPUT hooker Siyasanga Ngubelanga won the FNB Forward That Rocks award, for which Macala and Payi were also nominated. Ngubelanga scored six tries in this year’s FNB Varsity Shield.
There was scant consolation for WSU as Nkula beat Nkutu and Xakwana to the FNB Back That Rocks award. Nkula scored 83 points this season, including three tries, 22 conversions and eight penalty goals.
FNB CPUT – Tries: Asisipho Malotana, Mogamat Ameer Hendricks, Feghon-Leigh Snyders, Nathan Nkutu. Conversions: Snyders (2). Penalty goal: Snyders. Drop goal: Snyders.
FNB WSU All Blacks – Tries: Sakhele Ngeno, Eric Mcaphukana. Conversions: Litha Nkula (2). Penalty goals: Nkula (4).