Messi, who scored two goals in the 7-0 rout of Levante last week, did not emerge after the break and was replaced by Cecsc Fabregas in a game which saw goals for both clubs' big summer signings.
David Villa put the hosts ahead on 12 minutes with a wonderful volley from Arda Turan's cross and the former Barcelona man almost made it two soon after only for Gerard Pique to block his effort.
That allowed Neymar, on as a second-half substitute, to score his first Barcelona goal, meeting Dani Alves' hanging cross at the back post with a smart header on 66 minutes.
Both keepers made smart saves in a stretched end to the game to ensure neither side will take an advantage into next Wednesday's second leg at the Nou Camp.
On Messi's injury, Barca boss Gerardo Martino said: "He picked up a knock and when a player has an injury or a knock which impedes them from playing it does not make much sense for them to stay on the pitch."