The Egyptian striker, who joined Wigan in the summer on a one-year loan from Zamalek, scored ten goals for the Latics during the league's first term.
However, a severe drop of the player's form coincided with the team registering just two wins out of their last 17 Premiership games.
"Since we've lost Zaki, we look as if we don't have a cutting threat any more to score a goal and unfortunately if you can't score - you are always going to be up against it," Bruce told Sky Sports.
Bruce is convinced that despite the high expectations after Wigan's start to the season, finishing twelfth should be considered an achievement for a club of their calibre.
"We must remember who we are and what we are," the former Birmingham City boss added.
"For the last two seasons before this one we've been fighting relegation and going to the last game of the season and the second last so there's been a bit of progress thankfully."
With one Premiership round to go, Wigan are currently in twelfth position in the table with 42 points.
No Deal
In the meantime, it looks as if Wigan are not willing to make Zaki's move to the JJB Stadium permanent.
According to BBC Arabic, the club have announced that no new deal will be made to prolong the 26-year-old's stay at the club.
Relation between the player and the Wigan board and coach deteriorated after Zaki failed to return on time from international duty on a couple of occasions.