The Mali forward, 28, scored what proved to be the winning goal in the 60th minute and celebrated the goal by pointing to his skin in response to a section of the home fans who had targeted him throughout the match.
He was shown a yellow card for the reaction and after the abuse continued he tried to leave the pitch, pointing his thumbs down to the crowd, but was restrained by his team mates for a number of minutes.
Porto coach Sergio Conceicao was eventually forced to substitute Marega in the 72nd minute.
"We are completely indignant," Conceicao told reporters.
"They insulted Marega since the warm up. We are all a family here, regardless of our nationality, skin colour, height or the colour of our hair and we all deserve respect. What happened here is outrageous.
"I know the fans here are very passionate about their club and many fans are not represented by some of the people who were in the crowd today."
Marega later posted a message on Instagram calling the supporters who targeted him as "idiots" and also criticising match referee Luis Godinho.
"I'd also like to show my thanks to the referee who did not defend me and who gave me a yellow card for defending the colour of my skin. I hope I never meet you on a football pitch ever again. You are a disgrace," he added.
The league's organising body Liga Portugal condemned the chants.
"Liga Portugal does not agree and never will with acts of racism, xenophobia or intolerance that jeopardize the dignity of footballers or any human beings," said a statement on the organisation's website.
"Liga Portugal will do everything to ensure that this episode and all other racist incidents do not go unpunished.
"We believe this is a fight where your team's colours do not matter and everyone must come together to eradicate this scourge on the game."
Porto's director of communications Francisco Marques added on his own Twitter account: "Marega was fed up and left the pitch and Porto was forced to make a substitution due to racism."
Portuguese newspaper A Bola reported that no Porto players spoke to the media after the game in solidarity with Marega.
Vitoria coach Ivo Vieira said he did not want to comment on the incident as he was not certain what had happened.
"I prefer not to speak about a situation without being aware of all the facts. But if the player was provoked, then he should not have been," he said.
Porto are second in the Portuguese top flight, trailing leaders Benfica by a point after 21 games.