Neither player featured in the squad for PSG's Ligue 1 fixture against Clermont on Saturday, and there had been fears that the duo could miss out on the clash with Club Brugge on Wednesday night.
However, Pochettino has said that Messi and Neymar did not feature against Clermont after returning late from international duty and would be available for the team's European fixture.
"They came back to Paris on Friday night and trained today. I'm happy because even if they're tired, they don't have any physical problem. They will be here for Wednesday's game," Pochettino told reporters.
Neymar has only played 66 minutes of football for PSG at the start of the 2021-22 campaign, while Messi made his debut for the club off the bench against Reims before the international break.
The French giants will also take on Manchester City and RB Leipzig in Group A.