Gomez scored his 28th goal in 32 games on Wednesday when his 90th-minute strike in their Champions League Round of 16 tie gave Bayern a valuable 1-0 win in the first-leg in Milan.
As the Bundesliga's top scorer with 18 goals in 21 league matches this season, including three hat-tricks in the German league, Gomez has finally justified the 30 million euros (41 million US dollars) Bayern paid for him in 2009.
He will have another chance to shine at Munich's Allianz Arena on Saturday night when Bayern host Bundesliga leaders Dortmund looking to close the 13-point gap behind the German league's top team.
Last season, his first at Bayern, was far from convincing as he scored just ten goals in 21 matches and struggled for confidence in front of goal.
Van Gaal has often criticised Gomez in the past for his lack of finishing, but the softly-spoken son of Spanish immigrants is finally paying back some of the faith Bayern showed in him.
The Dutch coach insists his criticism of Gomez was misinterpreted in the German media as the 25-year-old re-finds his form.
"There is a misunderstanding on this subject," said van Gaal.
"I always select the best possible team and, believe me, Mario plays much better this season than he did last year."
Having been a substitute against Inter in Madrid last year when the Germans were comfortably beaten 2-0 in the Champions League final on Jose Mourinho's swansong as coach of the Italians, Gomez was superb in Milan on Wednesday.
Last season he found himself on the bench for both club and country, but this year he is taking his chances.
None more so when he rounded Inter goalkeeper Jose Cesar and slotted home with almost the last kick of the game in Milan.
"It is my most important goal in the Champions League," said Gomez.
"I just knew I’d get another chance, even if it wasn’t until the last minute."
His form is keeping veteran Miroslav Klose on the Bayern bench and with Croatia striker Ivica Olic injured, Gomez is now a first-choice.
After Liverpool expressed an interest in taking Gomez on loan at the start of the season, chairman Karl-Heinz Rummenigge over-ruled van Gaal to keep the striker in Munich.
"I always believed in him," agreed Bayern president Uli Hoeness.
"We have waited a long time to see him play at this level for Bayern.
"It was pointless to think of him leaving."