Having shipped 10 goals without reply in their first two top-flight games the Latics seemed ripe for a Carling Cup upset against the unbeaten League One side at Victoria Park.
But Sam Collins' third minute own goal set the visitors on their way before a stunning 76th minute free-kick from Gomez effectively snuffed out the home side's hopes.
It was just what Roberto Martinez - who made six changes to the side mauled by Chelsea on Saturday - had asked for, but there were times in the game when his side looked far from fluent.
And Martinez will know it might have been different had his goalkeeper Ali Al Habsi not pulled off a stunning fingertip save to deny Joe Gamble in the 28th minute.
There was much fortune about Wigan's opener as Collins and Steve Caldwell appeared to connect with a free-kick from Hugo Rodallega, with Collins credited with an own goal.
Evan Horwood got in with a well-timed header to deny Hugo Rodallega a clear run on goal as Wigan continued to enjoy a sustained period of possession.
But the home side fashioned their first chance in the 14th minute when Paul Murray struck a dangerous, bobbling shot which Al Habsi did well to hold first time.
Steve Haslam had to be on his toes in the 21st minute to chase back and stop a dangerous counter-attack by Rodallega, who paid the price for indecision on the edge of the box.
Hartlepool almost grabbed an equaliser in the 26th minute when Al Habsi failed to deal with a high ball into the box and Joe Gamble's attempted lob from the rebound sailed inches wide.
Two minutes later space opened up for Gamble again, who ran at the Wigan defence then unleashed a powerful 25-yard drive which Al Habsi did superbly to flap over the bar.
Andy Monkhouse should have done better with his 35th minute drive which flashed wide of target after Al Habsi had flapped a cross from Antony Sweeney into his path.
Martinez's men were suffering and relieved to see the final whistle, after which they regrouped to snuff out the threat from Pool, who had entered the game undefeated this season.
After a quiet start to the second half Rodallega had the first chance on the hour when he made space 20 yards from goal and hit a low shot which was deflected out for a corner.
With Wigan still holding onto their lead, Martinez made two changes in the 65th minute, introducing Victor Moses and James McCarthy for Rodallega and James McArthur respectively.
And in the 72nd minute Moses set up a good chance for Gomez, who flicked a shot with the outside of his left boot which flashed across the face of goal.
Spaniard Gomez finally breathed fire into Wigan's woeful start to the season in the 76th minute when he sent a stunning 25-yard free-kick in off the underside of the bar.
Wantaway star Charles N'Zogbia, reportedly on the brink of a move to Birmingham, was introduced by Martinez for the last 11 minutes in place of Mauro Boselli.
And with four minutes to go Moses ensured a rather flattering look about the scoreline when he fired past helpless home keeper Scott Flinders from the edge of the box.