The Brazilian had his head in his hands and appeared to be in tears as he was carried off the pitch, leading to fears he could face a long spell on the sidelines.
The 26-year-old was attempting to play a ball in the 76th minute and after a tangle with Marseille midfielder Bouna Sarr, he landed awkwardly on his ankle and fell over in pain.
PSG were up 3-0 at the time of the injury and won the match by the same scoreline, despite having to play the rest of the match with 10 men after using all of their substitutions.
First reports from the American Hospital, where Neymar was treated in the company of team-mates Maxwell and Marquinhos, were positive for the star.
Neymar was cleared of suffering a fracture or serious sprain in his ankle, and his health will be monitored in the coming 48 hours.
At the very least he is expected to miss a week of action for PSG, with further tests expected to determine the severity of his injury.
With their talisman's status in doubt and just 10 days until the match at Parc des Princes, PSG's chances of advancing to the quarter-final have become even more slim after having lost 3-1 to at the Santiago Bernabeu on February 14.
Neymar posted a picture of his ankle in a brace after the match to his Instagram account, with the message: "Ended up like this today."
He gave no indication of the severity of the problem.
Team-mates Edinson Cavani and Thiago Silva both spoke out over the injury after the final whistle, and expressed their hopes that the Brazilian has not been seriously hurt.
"It's normal to worry about Neymar and see how his situation is. And if there is an injury, it's normal to worry about it," Cavani signalled to Canal+.
"But we are always positive. And I hope he too. I hope everything is going well. That he can recover as soon as possible and be with us in the next matches."
Silva added: "It's a pity that at the end we lost a very important player for us. It's a shame, because it's not football.
"The referee should have intervened. Neymar plays and is happy to play. It's true that things like that happen. If it's serious? I think so, because it swelled up quickly. I am not a doctor, but I think he will be unavailable."
Boss Unai Emery was more optimistic, however, stating in his press conference: "First tests in the dressing room show he has a sprained ankle. We will conduct other test to be more precise. If I have to make a guess about [his availability for] Real Madrid tonight, I'd say he would be present."
Neymar has scored 20 goals in 20 Ligue 1 matches this season, his first in the French top flight after moving from Barcelona in a world-record summer transfer.