The on-loan Egypt striker took his tally for the season for 11 goals after scoring from the penalty spot a minute before half-time after Andy O'Brien's challenge on Henri Camara.
Latics boss Steve Bruce said: “Anyone who has seen us will know it is no fluke we are in the top half of the division.
“Our aim is to stay there if we can. There a lot of big clubs down near the bottom so it is great for a side like ours to be punching above our weight.
“Bolton have done it (played in the UEFA Cup), Blackburn have done it. Why can’t it be our turn?.
“In the calendar year we have taken something like 58-60 points. It is a fantastic achievement from the players but we are not going to get carried away.”
Bruce offered a tribute to the Egyptian forward Zaki, who has had some anxious domestic business to attend to.
“The kid has had a tough time,” said the Wigan boss. “He has a sick child.
“We will continue to try to help him. Thankfully his daughter is now okay and that has put his mind at rest.
“He is getting back to his best and is strong as an ox. He has unbelievable energy levels.
“Amr’s ended up with a bit of a lump on his eye but he can stand his corner.”
Wigan's victory was a tribute to their resilience and good organisation.
They lost goalkeeper Chris Kirkland to a groin problem in the warm-up and Mike Pollitt took the jersey.
But then they were hit with another injury blow when Emile Heskey limped off in the first half.
Wigan were good value for their victory, although Danny Shittu came close to equalising in stoppage time.
Bolton looked jaded after their efforts against Liverpool on Boxing Day when they suffered a 3-0 defeat and were jeered off at the end.
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