Summer signing Messi hit the angle of post and bar with a free-kick in the first half and forced a save from Anthony Lopes but was below his best.
With the score at 1-1, he was replaced by right-back Achraf Hakimi and did not look happy at coming off.
Messi was given a round of applause, but not a standing ovation by his fans.
The 34-year-old, who left Barcelona this summer, did not stop but briefly said something to boss Mauricio Pochettino while walking past him to the bench.