Pique defended the Portuguese player, who bore the brunt of the criticism for the team's 4-0 thrashing by Paris St Germain in the Champions League last-16 first leg and was loudly booed in the team's next game against Leganes when he was substituted off.
He was dropped from the starting line-up for the second leg against PSG but came on as a substitute in the historic 6-1 turnaround which saw Barca reach the quarter-finals.
Gomes was greeted with more whistles when he came on in the 74th minute against Valencia on Sunday but 15 minutes later sealed victory by turning Neymar's cross in from close range, although he chose not to celebrate the strike against his former club.
"I'm in total disagreement with the people who boo players, they'd be better off staying at home," Pique told reporters after the game on Sunday.
"It's intolerable and I think treating any player like that before they come on the pitch doesn't help anyone. People need to take a good look at themselves.
"It's one thing if someone plays badly and then the people whistle to show their discontent but quite another to whistle before they come on because it kills their confidence."
Gomes was a surprise summer signing from Valencia for 35 million euros ($37.6 million) plus add-ons and has struggled to adapt to the Spanish champions, often looking out of place in the team's midfield and out of sync with the rest of the team.
Luis Enrique has persisted with Gomes despite the continued criticism and at one spell in the season preferred the him to Ivan Rakitic, although the Croatian has since won his place in the team back at Gomes' expense.
"I'm so pleased he scored, it was the happiest moment of the game," said the coach.
"I already know how good he is, he's huge, he's strong and has great talent. He's going to be a very important player to Barcelona's future."