Fabregas opened the scoring in the Gunners' 3-1 win over Burnley on Saturday but had to be substituted shortly afterwards.
Arsenal boss Arsene Wenger: "He has a hamstring problem and how big the damage is we don't know yet because it's too early.
"We have to make a late decision over whether he plays on Tuesday, certainly. It is the same hamstring [he hurt earlier in the season]."
Arsenal must overturn at 2-1 deficit from the first leg against the Portuguese side.
Wenger also hailed the performance of Theo Walcott.
The winger came in for criticism after his performance for England in midweek, but responded with an impressive display and the crucial second goal to put Arsenal back in front after David Nugent's equaliser.
Wenger said: "Theo Walcott gave you the great response you waited for.
"He does what a player has to do - not talk in the newspapers and let your performance talk on the pitch.
"He didn't answer any critics other than with a good performance today and that's what you want from a player. That shows he is mentally strong.
"I was quite sure he would respond with a good performance but you never know, it affects you when you get criticised. The way he answered that at his age is remarkable."
Fabregas Could Miss Porto TIie
