City's Bernardo Silva and Mateo Kovacic both misfired in the shootout to put Madrid in the driving seat
The fourth-seeded Spaniard, who will play either Argentine Facundo Bagnis or French qualifier Kenny de Schepper in the second round, played flawless tennis throughout, making only three unforced errors in a one-sided match.
Nadal, who turns 30 next week, has won two titles on clay this season, including the Monte Carlo Masters in April.
He ended his opponent's misery with a trademark crosscourt forehand winner on his second match point on Court Suzanne Lenglen.