Messi came off the bench in the 66th minute, replacing Neymar, as PSG eased to the Ligue 1 win.
The Argentine’s debut drew global attention but Real Madrid target Kylian Mbappe stole the show with a double for the Parisians.
Messi had not played since Argentina’s Copa America triumph in early July and had been held back as he improved his match fitness despite signing for PSG three weeks ago.
The 34-year-old’s impact off the bench was positive, although he was introduced with PSG already 2-0 up and didn’t produce any decisive moments.
“Messi? He’s happy too with the squad and with his teammates,” Pochettino told reporters after the game.
“He wants to continue working, and I’m sure well be even better.”
Pochettino added: “It was important to win and to get the clean sheet, it will help build our confidence.
“Four games and 12 points is great for the international break. So yes I’m really, really happy.”
PSG are top of Ligue 1 with a 100 per cent record and face Clermont after the international break where Messi may be in contention for a starting debut.