The 19-year-old Spaniard recovered from losing a lung-busting opening set, rattled through the next two and then held off a brave Puerta fightback to claim his first grand slam title.
In doing so he also became the first debutant since Swede Mats Wilander in 1982 to win the men's singles at Roland Garros.
Puerta, who this time last year was still serving a doping ban, played inspired tennis early on and looked capable of emulating countryman Gaston Gaudio's triumph here 12 months ago.
But Nadal would not be denied.
Soaking up everything Puerta could muster, he eventually ground the gallant Argentine into the dust, saving three set points in a gripping fourth set before Puerta sent a forehand wide on Nadal's first match point after three hours 24 minutes.