Midfielder Fabregas is expected to miss the next two weeks after injuring his right leg in Tuesday night's Champions League defeat at Braga.
The problem follows a troublesome strain in his other leg, which he suffered in September's Premier League draw at Sunderland.
"Cesc is a ball giver and Owen was more a runner," said Wenger.
"The strength of Owen was more based on his pace and the timing of his runs.
"Cesc is more a playmaker, so he doesn't need to sprint as much.
"That's what is remarkable in Cesc's case: usually, people who are exposed to hamstring injuries are sprinters like Owen or Ryan Giggs but Cesc is more a stamina player and that's what puzzles me a little bit.
"I'll do what is right for him and for the club but I will listen, of course, to medical people.
"It is a hamstring and I remember Ryan Giggs has gone through that his whole career but it didn't stop him from making a big career."
Wenger revealed yesterday he may ration Fabregas' playing time for the next couple of months in order to prevent his star player suffering a recurrence of the injury.
"We will consult every specialist we can," he said.
"But, at the end of the day, it doesn't stop him from being injured."