The 26-year-old had a blistering start to the season after joining from El Zamalek, with eight goals in his first 10 matches, but he has not scored from open play since mid-October and his last goal came on Dec 28.
Zaki has been affected by injuries but it was a souring of his relationship with Bruce that has cost him a permanent deal.
In early April he was fined for the fourth successive time after returning late back from international duty, leading to Bruce labelling the player "the most unprofessional I have worked with".
Zaki has played only three times since then and the knee injury sustained at West Brom just over a week ago means he has almost certainly played his last game for Wigan.
Bruce also felt the player allowed his head to be turned by links with Real Madrid, Chelsea and Liverpool after making an early impact on the Barclays Premier League.
"I've made my decision already, a letter has gone to his club, we will not be taking up the option to sign him when his loan ends," said the Wigan manager.
"The writing has been on the wall for a while now but it's a shame, it really is.
"There was no doubt Zaki had the world at his feet last October when he scored those two goals against Liverpool at Anfield.
"He had a wonderful chance over here but he was badly advised I think, he listened to the wrong people.
"If he had listened to the people he should have done - his adviser is a decent fella - he would have been okay.
"It's a shame it's worked out this way, he set us on fire with those goals earlier in the season.
"But Zaki hasn't scored from open play since Liverpool. We've missed him in that respect, but there you go."
Bruce also has other major decisions to make as Zaki's compatriot and fellow striker Mido is coming to the end of his loan spell from Middlesbrough.
Antonio Valencia may also have played his last match for Wigan after missing Saturday's defeat at Stoke with a hamstring injury.
The Ecuador winger has been linked with a number of clubs over the last year and is destined to leave the JJB Stadium in a big-money deal this summer.
"Antonio will inevitably go, that will be very difficult for us. Now we have to go and find some new players," said Bruce.
"We've got to do our homework over the summer, find two more strikers from somewhere, we'll try everywhere.
"We'll get good money for Antonio but that won't necessarily make us better because we're losing such a talent.
"For example, we could get three players in with that money, improve the squad overall, but maybe not make us a better team."