The Mexican has been sidelined with a serious knee injury.
Marquez was hooked early in the second half and replaced by club captain Carles Puyol, who was being rested for the return leg at Stamford Bridge due to being on a yellow card.
The 30-year-old Mexican was trotting up to the halfway line courting the ball at his feet when he was forced to knock the ball out of play before falling to the ground in obvious pain.
Further tests will be carried out on Marquez on Wednesday, but it has been confirmed that he will not see any first-team action for the rest of the season due to meniscus damage in his left knee, according to Sky Sports.
Barca suffered an additional blow when Puyol was booked for a tackle on Michael Essien, ruling the skipper out for the trip to London.
Stephen Crawford, Goal.com