Wijnaldum was deployed in an attacking right-sided role, with Messi ruled out after his recent COVID-19 positive test.
The runaway Ligue 1 leaders managed just three shots on target in a frustrating game, having 68.4 per cent of possession but struggling to make their dominance count, and Pochettino lamented their slow start after the final whistle.
PSG required a late strike from substitute Thilo Kehrer to take a point, having trailed for over an hour after Lucas Paqueta's early goal.
Wijnaldum had only one shot, which did not hit the target, while on the opposite flank Kylian Mbappe failed with five shots, although two hit the goal frame.
Netherlands international Wijnaldum, who signed for PSG last June, had a 95.6 per cent passing accuracy rate, but he struggled to pose a substantial attacking threat to mid-table Lyon.
Asked after the game to assess Wijnaldum's struggles, Pochettino defended his decision to field the midfielder in such an advanced role, and in a variety of positions during his short PSG career.
Pochettino, quoted in L'Equipe, said: "It is also a question of balance, of players available. I don't think it's a question of position but of states of form.
"Wijnaldum has a lot of experience, he has been at great clubs. He is used to playing in different positions."
PSG mounted its recovery after substituting central midfielders Leandro Paredes and Ander Herrera on the 69-minute mark, with Wijnaldum following them off the pitch late in the game.
"When we changed, we were looking for freshness. The introductions of Thilo Kehrer, Xavi Simons and Edouard Michut brought energy and enthusiasm," Pochettino said.
"They played part in the equaliser and they carried the team, so I'm happy."
PSG remains 11 points clear at the top of the Ligue 1 table, but has now drawn four of its last five league games.