OM won the Ligue 1 encounter 1-0 thanks to Greenwood's goal. However, the former Manchester United forward was taken off by Beye on 66 minutes.
There are doubts about Greenwood's position at OM after the dismissal of coach Roberto de Zerbi, who was his biggest champion inside the club.
Explaining the substitution, Beye stated: "I put Mason as a striker, but I wanted him to come and fix the left centre and Methalie, to give room to Quinten Timber and Timothy Weah.
"I knew Mason wasn't a player who stayed in the middle. But there was this scuffle where he received a yellow card, and as Mason is an instinctive player, I didn't want us to end up with 10 in that match. It was a precaution I took at that moment.
"We had planned to give Amine (Gouiri) 30 minutes to allow him to come back. He did two days of high-intensity training, which is a very good thing. We managed that moment well. Mason gave us a fantastic goal and I think it's a group victory."