The Belgian’s injury-plagued campaign took another blow when he pulled up as he played a through pass just before half-time and he now looks set for a period on the sidelines.
John Stones also had to come off, though his problem is thought to be less serious.
VIDEO: Mahrez post-match reaction
“Kevin may be out for a while,” said Pep. “It is his hamstring. When we play 25 games in 93 days, it is hard and becomes a physical issue.
“We don’t give players time to recover. John's is not a big problem – more of a precaution.
“We play a game, then after, when they are not recovered, we play another game.
“There is only a short amount of time and it is very demanding.”
City dominated Bournemouth from start to finish, with the hosts’ ultra-defensive formation designed to frustrate the champions.
The Blues boss said he was, however, delighted with what he described as one of his team’s best performances under his tenure.
“It was an incredible performance, one of best played in our time together,” said Pep.
“Ten players behind the ball for every moment, second balls, set pieces, everybody focused on controlling… it is a joy and pleasure to be part of this team.
“Thank you to my players who were absolutely incredible. It doesn't matter what happens at the end of season, these players deserve my admiration.
“We didn’t concede one shot on target and in this kind of stadium it’s almost impossible to do that with their throw-ins, set-pieces and fast players.
“Ten players in the box is almost impossible to play against, but for two or three seasons, we have worked on this and now we are starting to see things coming to fruition.
“We have a lot of injured players, but everybody is pulling together.”
The Catalan also praised David Silva and Oleksandr Zinchenko, who both played a part in Riyad Mahrez’s winning goal.
“David was incredible,” he said. “In first half of the season we qualified for the Champions League and he was one of the main reasons.
“After that, he had an injury and took time to get his pace back. For three or four games in a row he has been incredible.
“Zinchenko is definitely important to us. He is playing top. With the ball, without… his attention is excellent.
“Players play because they deserve it. Oleks was committed, smart, intelligent and he understands everything – he has incredible quality.
“But I repeat, I am so delighted with all my players.”