Eight-time champion Nadal, bidding to become the first man to win five Roland Garros titles in a row, beat US wildcard and world number 279 Robby Ginepri 6-0, 6-3, 6-0.
It was Nadal's 60th win at the French Open against just one loss.
World number one Nadal kicked off his campaign yesterday on the secondary Suzanne Lenglen court while title rivals Djokovic and Australian Open champion Stan Wawrinka were handed top billing on the main Philippe Chatrier arena.
Despite the controversy, it was business as usual for Nadal who fired 27 winners past Ginepri, a semi-finalist at the 2005 US Open whose challenge was undone by 41 unforced errors.
"It doesn't matter where I play," said Nadal who next faces either Paul-Henri Mathieu of France or highly-rated Dominic Thiem of Austria.
"It's always a pleasure and an honour to play at Roland Garros, on Chatrier, Lenglen or any other court. This place has given me unforgettable emotions."
During a match interrupted by rain, the 27-year-old Serb was at his charismatic best, delighting the Philippe Chatrier crowd by sharing a drink with a ballboy as they sheltered beneath an umbrella.
Djokovic, widely regarded as the favourite to dethrone Nadal having beaten the Spaniard in Rome two weeks ago, next faces French hope Jeremy Chardy.
"I played for most of the match quite solid. The end of the match was not so nice from my side because I dropped my serve twice," said Djokovic.
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