Bakayogo appeared to catch his studs in the turf with no other player near him and was replaced by Jamie McAllister who minutes later was himself replaced by Matteo Lanzoni.
The set back was the latest in a series of injuries to loan players since the start of this season including Sam Johnston, Fraser Fyvie, Andy Williams and Liam Fontaine.
Speaking about the injury manager Gary Johnson said:"Zoumana said he just felt his knee crumble under him. It was innocuous - he just turned and he felt it.
"Jamie McAllister couldn't catch his breath, so I couldn't wait for him to have ten minutes on the side to catch his breath. We trust Lanzoni, and when he came on, I thought he did very well in coming on as right-back and Luke did very well in adjusting as a left-back. So maybe we found our left-back!
"We brought in Zoumana Bakayogo for Liam Davis, who we left at home because he was injured. So there's maybe another little left-back hunt again in the next week or so."