Genk went into the game knowing a draw would be enough to win the title but they allowed Standard to dominate possession early on and the visitors opened the scoring.
Standard's French defender Eliaquim Mangala netted in first-half stoppage time after Genk failed to clear a free-kick.
The hosts picked up the tempo after the break but had to wait until almost 10 minutes from time for Nigerian Nwanganga, who had only been on the pitch for two minutes, to head home from a corner.
Genk goalkeeper Thibaut Coutois then pulled off a couple of crucial saves in the final minutes.
"This is an unexpected title," said Genk coach Franky Vercauteren, who has also managed rivals Anderlecht and was briefly in charge of Belgium.
"We really took a hit from their goal. At the break, I just insisted that one goal for us would be enough. The players understood the message. Kennedy proved decisive but Courtois really saved us at the end."
Standard only narrowly sneaked into the end of season playoffs and then won eight of their 10 play-off matches, drawing the other two, but the title proved just beyond their grasp.
Genk and Liege finished the season level on 51 points.
After the regular season, each club's points were halved. Liege had an odd number of points and benefited from a rounding up of their tally for the start of the playoff matches.
Genk's total was not rounded up meaning if the two teams were level in the table Genk were considered to be ahead.
Standard may still end the season with a trophy as they play Westerlo in the Belgian Cup Final on Saturday.
Standard and Genk have both qualified for the third qualifying round of next season's Champions League.
