Three goals in a 15-minute second-half spell from the home side turned the match around.
With two rounds to play Genk, who would have won the title with victory on Sunday, have 50 points to second-placed Bruges's 47.
Genk’s Sebastien Dewaest scored after just three minutes, getting onto the end of a long freekick as he ghosted through unmarked behind the home defence.
But Hans Vanaken, Lois Openda and Krepin Diatta all netted as the home side came back strongly after the break and they could have had a fourth had Vanaken not hit a 74th-minute penalty against the crossbar.
Genk, who last won the championship in 2011, pulled one back three minutes from time through Zinho Gano and then hit the woodwork through Mbwana Samatta in stoppage time.
Both clubs play again on Thursday, with Genk away at Anderlecht and Bruges travelling to Standard Liege.
(Reporting by Mark Gleeson; editing by Tony Lawrence)
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