The midfielder was forced off in the first half on Saturday after earlier putting the Gunners ahead and the problem is with the same hamstring which sidelined the Spaniard for three weeks earlier in the season.
Wenger will continue to assess his captain in the build-up to Porto's visit, but he is willing to take a risk on Fabregas if neccessary.
"I'm ready to take the gamble," said Wenger, whose Arsenal side must overturn a 2-1 deficit from the first leg. "But if there is more than a 50 per cent chance of his hamstring going I will not take it."
Wenger also praised Fabregas' progress this season, with his goal against Burnley the 14th he has scored in the Premier League this term.
Wenger added: "You look at the Fabregas numbers and they are amazing - 14 goals and 15 assists. He's a fantastic player with a fantastic attitude and commitment.
"And what people forget, an unbelievable work-rate too. This season he has taken a big step forward, massive. At 22 years of age he has matured."
Arsenal 8/13, Draw 13/5, Porto 4/1