Neymar was forced off inside half an hour in Instanbul with match still scoreless as PSG faced the Turkish side in the second match of the group stage
The winger was forced out after 26 minutes, having previously come off the pitch a few minutes earlier due to an apparent injury.
He was replaced by Pablo Sarabia, who joined Kylian Mbappe, Moise Keane and Angel Di Maria in the PSG attack, with Neymar becoming the first PSG player to be substituted in the first half in a Champions League game since Thiago Motta against Manchester City in April 2016
Wednesday's injury comes after Neymar recently overcame a back issue after previously dealing with a calf issue.
The Brazilian winger has made four appearances for PSG in Ligue 1, scoring two goals as the defending champions sit atop Ligue 1 with 20 points through eight games.
He also started PSG's Champions League opener, earning a yellow card as last year's runners-up fell to Manchester United at the Parc des Princes.
Neymar scored three goals in seven appearances throughout PSG's run to the final last season, featuring in the finale as they fell to Bayern Munich in a 1-0 defeat.
While Champions League success has eluded Neymar and PSG since he made the move from Barcelona to France in 2017, the Ligue 1 giants have claimed three league titles, two Coupes de France and two Coupes de la Ligue.
The winger's injury could have a major impact on PSG's season, with the Ligue 1 side set to visit last season's semi-finalists RB Leipzig in their next Champions League clash.
Before that, though, they'll visit Nantes in Ligue 1 play, with their opponents currently sitting 15th in the league.
Any extended absence could also see Neymar miss matches for Brazil, with the Selecao facing World Cup qualifiers in November.