A Peter Kennedy free-kick brought Wigan their tenth straight win as they increased their lead at the top of the Nationwide Division Two table to 12 points.
Their narrow win was more decisive than it looked as they always had the edge.
Bristol City, the second division's leading scorers, were never given the room to build the careful attacks which are the cornerstone of their game.
Kennedy's chance came early in the second half and his left-footed free-kick was his first goal for the club in 53 games.
This was always a game to shape the second half of both sides' seasons, a fact City's manager Danny Wilson acknowledged before the start.
A City win he said "Would bring joy to all managers in the top half because it would bring Wigan back towards the pack".
That proved to be wishful thinking as Nathan Ellington so nearly fired the Latics ahead in the sixth minute after being sent clear by his strike partner Andy Liddell.
His powerful shot was matched by a sharp save as Steve Phillips threw himself to his left.
Midway through the half a slip by home skipper Tom Doherty gave Ellington another chance to break the deadlock but this time he slammed a left-foot shot against a post.
Scotland's coach Berti Vogts turned up to watch Bristol City's Scott Murray but the winger had few chances to add to his 17 goals.
He came closest when Danny Coles' long ball sent him clear only for Jason De Vos to make an incredible tackle on the 18-yard line.
Matt Hill, put in by Doherty, had a better chance in the 30th minute but the ball ended up in the stands as he lost his balance.
There was worse to come for Hill as it was his mistake, giving the ball to Ellington, which led to the goal.
Both players hared towards City's goal, Hill fouled Ellington just outside the box and Kennedy's left foot bemused the wall.