Zaki's dispute with Bruce ended after he was fined four weeks' wages as a result of his failure to return from international duty on time.
The Egypt striker, who is nursing a hamstring injury, is now in line to partner his compatriot Mido upfront in Wigan's Premier League clash against Blackburn on April 26th.
"He's back, has apologized, now it's time to let him get over this injury," Bruce told the Evening Post on Thursday.
"I think he will be available for Blackburn and I'd have no qualms picking him – I have to think about the team.
"We haven't got the biggest of squads to start with, and could have done with Zaki against Arsenal when Mido had to come off.
"My job is to get the best out of the games we have remaining this season.
"If we had bundles and bundles of players available, it might be a different scenario with Zaki, but we haven't. So I'll do what I think is best for the team."
Zaki, who joined Wigan from Zamalek on a season-long loan last summer, is Wigan's top scorer with 11 goals in all competitions.
However, he hasn't found the net since converting a penalty against Bolton Wanderers last December.