Messi was given a round of applause, but not a standing ovation by his fans.
Lionel Messi made his home debut for Paris St-Germain but was replaced in the second half as they went on to beat Lyon to make it six wins from six.
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.
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.
Another PSG substitute, Mauro Icardi, ended up scoring the injury-time winner in the Ligue 1 game, as he headed in Kylian Mbappe’s cross.
Lucas Paqueta swept in Karl Toko Ekambi’s cross to give Lyon the lead.
But Neymar equalised with a controversial penalty. He appeared to pull back Malo Gusto in the box but the teenage Lyon defender was penalised instead, with a spot-kick given.
Neymar waited for Lopes to move before slotting in.