Both sides had their share of chances at the Peter Mokaba Stadium in Polokwane, with the hosts dominating the first half and Spurs getting back into the match after several changes at the break, but a stalemate was on the cards until the last-gasp winner.
Spurs had an early scare when Tom Huddlestone went down injured in the first minute, but the midfielder was fit to continue after treatment.
Siphiwe Tshabalala twice went close for Chiefs in the opening 15 minutes, while Lehlohonolo Majoro could have opened the scoring on two occasions as Tottenham were placed under heavy pressure before the break.
Harry Redknapp made seven changes for the second period and two of the reinforcements, Gareth Bale and Peter Crouch, almost combined to put their side ahead, the England striker's header only denied by a superb save.
Bale had his chances of his own to put Spurs on the scoreboard, twice missing from tight angles before a 90th-minute volley drew another smart stop.
That left Lebese to steal the limelight moments later when he finished off a quick counter to secure the win.