Manager Unai Emery hinted earlier this week that Neymar could recover in time to face Real Madrid in the Champions League on March 6, but the decision was then taken for him to instead go under the knife in his homeland.
Asked about the club's decision, Al-Khelaifi insisted that they were left with no other option.
"We are very sad about this news," he told reporters following Wednesday night's Coupe de France win over Marseille.
"But [surgery] is the best decision for him, for the club, for the national team of Brazil. We do not have a choice. We made the decision together. It's not good news, but the players showed [on Wednesday] that they wanted to play harder together.
"We will do it together, with the players and the fans. The match against Real Madrid is very important. It's the game of the season, as we want to qualify for the quarter-finals. We will qualify. We have the team and the players who are able to do it. We will work together."
Neymar had scored 28 goals in all competitions and set up 16 more prior to suffering his potentially season-ending injury.