The spectator surged from the crowd near Nadal as he was about to serve for the second set, leading 5-1.
Security personnel bundled him to the ground and quickly dragged him away. Another guard stood near Nadal, protecting him while the protester was subdued. Nadal later shook the bodyguard's hand before resuming play. The match was only briefly delayed.
Moments earlier, two people interrupted play by chanting while holding a banner in the upper deck of Court Philippe Chatrier until security led them away.
Christophe Fagniez, the tournament's director of operations, later said: "The situation is under control, it's in the hands of the police."
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Nadal went on to beat Ferrer 6-3, 6-2, 6-3, becoming the first man to win eight titles at the same Grand Slam event.
A male streaker wearing nothing but tennis balls and sneakers ran onto the center court and hurdled the net during the 2003 final where Juan Carlos Ferrero beat Martin Verkerk.
Federer brushed the man aside before security guards got close enough to intervene. After hopping the net, the man was tackled and jailed for questioning.