Coleraine missed out on a top three finish and a place in the Europa League by failing to win at Seaview.
Crusaders took the lead in the 77th minute when Michael O'Hanlon's shot was well saved by Gavin Cullen but the ball fell for Jordan Owens to drive in.
Coleraine got level when the referee ruled that Stephen Lowry's shot had crossed the line before the Crusaders defence cleared the ball away.
Ryan McCann's curling direct free-kick gave the Crues an 86th-minute winner.
The result meant Coleraine stayed in fourth place with Irish Cup finalists Crusaders two points behind them in fifth.
Crues boss Stephen Baxter again rested many of his established stars with the cup final against champions Linfield just seven days away.
However, some of the Seaview teenagers took the chance to shine in the first team.
Goalkepeer Jack McCrea saved a low shot by Lowry early on and he also got down well to turn Curtis Allen's shot behind for a corner.
The first goal eventually came when 17-year-old schoolboy international O'Hanlon attempted to curl in a shot from the left side of the penalty box.
Cullen did well, diving to his left to palm the ball away. However, it fell to striker Owens who had time to control before blasting in the breakthrough goal.
Lowry's equaliser would have been a lot more controversial if it had affected the result and the battle for European football.
Crusaders felt they had succesfully cleared the ball off the line but the assistant referee indicated it had crossed the line.
However, the Crues sealed victory with McCann's perfectly-placed free-kick.