The ball boy's quick throw to Martim Fernandes helped the defender find Gonzalez with a prompt throw-in. Gonzalez played a one-two with forward Pepe before sending it through to the box, with Pepe's right-footed shot going past the keeper near the far post.
The 59th-minute goal restored the hosts' lead, ensuring second-placed Porto's seventh win in eight league matches as they trail defending champions Sporting by three points.
Gonzalez handed the ball boy his MVP award after the match.
"We got another three points today thanks to him too. He'll get the tribute he deserves," Porto head coach Vitor Bruno told reporters.
"These boys are very important. It's also necessary for those who are on the sidelines and don't directly interact with the game to realise how they can help, even from the sidelines."
Porto, who held Manchester United 3-3 in the Europa League last week, will visit Sintrense in a Portuguese Cup match on October 20.