The match between Nadal and David Ferrer was in the second set when a shirtless spectator, wearing a white mask, leapt from the stands and onto the court brandishing a flare before he was wrestled away by security officials.
The protester had the words 'Childrens Rights' written across his chest in English.
The incident took place just in front of the VIP box on Court Philippe Chatrier where Olympic sprint champion Usain Bolt and Hollywood superstar Leonardo DiCaprio were sitting.
Nadal went onto to win the final, 6-3, 6-2, 6-3, and become the first man to win the same Grand Slam title eight times.
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Ferrer, who had been at the far side of the court, said he had been unconcerned over the incident.
"I didn't lose my focus," said the 31-year-old, playing in his first major final.
He then added with a smile: "I think Rafa was a little scared."
An AFP journalist later saw four people, all aged around 20 years, being led away from the stadium by security agents.
"We are protesting against the Taubira law (authorising same-sex marriages) because we fear for the future of our children," one of the four shouted out.
A police spokesman later told AFP that 12 people had been arrested.
"It is always regrettable," said Ysern.
"It did not last long because we saw that our security immediately handled the situation.