On the brink of dragging this tie into extra time, midfielder Vincent Pule turned into super-sub hero as he knocked in a cross by Amr Gamal to earn the Students just over R4 million.
With 15 minutes on the clock, Pule replaced Daylon Claasen and got the crucial touch to score just after Celtic made their first substitution in the 87th minute, in anticipation of extra time.
The result saw Wits coach Gavin Hunt complete his trophy cabinet with every top-flight silverware on offer.
On a muggy
Egyptian forward Amr Gamal nodded a header wide for Wits in the first serious threat by either outfit.
Until that opening, the travelling Celtic supporters of just over 100 clad in green-and-white provided the entertainment with their non-stop singing, clapping and dancing behind the Celtic goal, aided by a drumming crew in the main stand of the venue that was just over half-filled.
Wits did most of the probing. The defending league champions, uncharacteristically rooted to the bottom of the Absa Premiership table with a third of the campaign over, had the best moment to break the deadlock when Malawian menace Gabadinho Mhango broke through on the left.
His low cross was deflected on to the post by Celtic defender Wandisile Letlabika, and rolled across the goal-line as Daylon Claasen and Gamal failed to capitalise.
Coming into the game following a six-match ban for a spitting incident against AmaZulu in this city, Mhango was eager to get stuck in against his old teammates.
While he tricked on the left touchline, Claasen roved on the right, with Daine Klate lending support in a central role behind Gamal.
Apart from the potential own goal by Letlabika in the 26th minute, the defences were sharper than the attacks. The best from Celtic was a snapshot from Roggert Nyundu a minute earlier.
Wits coach Gavin Hunt retained the backline that drew 0-0 in their last game, a league assignment at Maritzburg United.
The back four of Nazeer Allie, Buhle Mkhwanazi, Thulani Hlatshwayo and Sfiso Hlanti, which formed the foundation of Wits’ championship glory last season, was seldom troubled in the opening period.
After the interval under cooler conditions, Celtic awoke from their slumber and got their crowd’s volume a few notches higher as winger Deon Hotto pushed forward stronger.
They threatened first with Victor Letsoalo’s header bouncing on to Darren Keet’s bar in the 63rd minute.
The excitement was short-lived and the affair reverted to a tight battle as the rivals rang wrong attacking numbers, highlighting the national scoring problem.
If there was hope, it lay in the foreigners as Gamal proved his class with a volley that Patrick Tignyemb tipped away for a corner in the 79th minute.
Otherwise it appeared that Celtic might do enough to hold Wits at bay and head into their third penalty shootout of the competition, let alone extra time, as Hlanti rifled a free kick into the night sky.
Letsoalo threatened to score at the other end, but Pule got the vital touch that crowned Wits champions of the league cup for the third time.