The Argentine World Player of the Year collapsed to the ground clutching the back of the knee after colliding with Benfica goalkeeper Artur in the 0-0 draw and looked to be in severe discomfort as he was taken from the pitch.
Barca said on their Twitter feed he had suffered bruising on the outside of the knee and would undergo further tests to determine the extent of the damage.
A statement said: "After shooting with his left foot the player fell to the ground with pain in his left knee.
"The player is now in the Nou Camp dressing rooms being treated by club medical staff."
Messi remains one goal short of German Gerd Mueller's record of 85 goals in a calendar year set in 1972.