The Spaniard was making only his third start of the season in the Barclays Premier League and was jeered early in the game for a few poor touches.
But he responded superbly with goals in the 58th and 68th minutes to turn things around after Sean Morrison had given Reading a 35th-minute lead.
The Royals looked to have snatched a point with a major stroke of luck in the 80th minute when Wigan keeper Ali Al Habsi dropped a wet and spinning ball against the bar that then rebounded against him and went in.
But Gomez had the last word two minutes into injury time to earn Wigan a 3-2 win that lifted them five points clear of the relegation zone.
The midfielder is only the third Latics player to score a Premier League hat-trick after Marcus Bent and Henri Camara, and Martinez believes he has been treated unfairly by some of the Wigan fans.
"The role Jordi had to play today [Saturday] was as unfair as you're going to get," said the Latics boss. "Because he missed the first two or three passes, all of a sudden the crowd let him know.
"I've seen it so many times and it's very difficult to compose yourself, and it would have been all too easy for him to hide and look away from the challenge. But that's not Jordi at all. Nobody deserved a hat-trick more today [Saturday] than him.
"It's not just the three goals, he always shows for the ball, he had another two great opportunities.
"The crowd were too vocal against him and I hope that today they realise that the only thing Jordi does is give his life for Wigan Athletic and to win football games. I hope we all realise that and he gets a bit of warmth the next time he's on the pitch."
In contrast, Al Habsi has been a huge hit since joining Wigan from Bolton in the summer of 2010 and he had made a brilliant flying save from Adam Le Fondre's header moments before his howler.
Martinez was more than happy to forgive his keeper, saying: "Goalkeepers are exposed to that, they're the last men, and it's just Ali doesn't do that, which is why you're so surprised.
"Minutes before he had the save of the game. Internally as a team you should be there to help your team-mate when he makes a bit of an error, which happens, it's a game of errors and you need to be able to overcome whatever situation comes your way.
"Today [Saturday] we showed that type of performance. In the first half we had a little bit of the feeling of something to lose.
"We weren't sharp or as effective as we can be, and to concede from a set-play and allow Ali to have a mistake, I think it was more our approach and our mentality, and we need to change that.
"But it was pleasing to see the players found a reaction and a way to overcome that. To give that win to the dressing room pleased Ali more than anyone.
"I think it's the time to thank him for the amount of times he got the team out of difficult situations with his outstanding performances."
To come away with nothing in such circumstances was a real blow to Reading, who arrived in the north west on the back of their first Premier League victory of the season against Everton last weekend.
Boss Brian McDermott was frustrated they could not see out the game but felt his side should have had a penalty for a foul by Maynor Figueroa on Jay Tabb when the score was 1-1.
"I thought we deserved a point, and I thought it was the least we were going to get," said McDermott.
"I think if the referee had given the penalty on Jay Tabb we would have gone on to win the game. Someone of Howard Webb's experience and quality, you would have expected him to get that one right.
"When you're 2-2 in the 92nd minute and we've got the ball, you've got to make sure you see the game out. If you have to take a point in this league then take it and move on.
"We have to learn quickly from that. We've seen out the last couple of games really well but unfortunately we haven't seen this one out."