The Catalan giants opted to keep their mercurial Argentine playmaker on the bench for their UEFA Champions League clash with Benfica on Wednesday, shielding him from picking up a knock in what was a dead-rubber for Tito Vilanova's side.
Messi was, however, thrust into action just before the hour mark at Camp Nou as Barca attempted to force a breakthrough in their final Group G fixture.
That decision came back to haunt them five minutes from time when Messi sprang clear but collided with Benfica goalkeeper Artur as he attempted to negotiate a route to goal.
The reigning World Player of the Year was able to get in an attempt on target, but collapsed to the ground clutching the back of his knee and was eventually taken from the field on a stretcher.
Barca confirmed after the game, which ended goalless, that Messi had suffered bruising to the outside of his knee but that he would be undergoing further examinations.
"After beating the offside trap Messi tried to dribble round opposing keeper Artur, who dealt him a blow, but Messi continued with the move," Barca said in a statement on their official website.
"After shooting with his left foot the player fell to the ground with pain in his left knee," the statement added.
"The player is now in the Nou Camp dressing rooms being treated by club medical staff."
Messi will be hoping to figure again in the not too distant future as he is sat on 84 goals for 2012, one behind Gerd Muller's record for a calendar year.