The Spaniard had described the clash as "one of the most dangerous first rounds" he was likely to face in an ATP 500 event, having seen his comeback stalled by illness and injury.
Following his return from a wrist problem that kept him out from June until September, Nadal contracted appendicitis in his second tournament back - the Shanghai Masters.
With Nadal acknowledging fitness concerns could keep him out of the ATP World Tour Finals in London next month, the world number three could barely have hoped for a more comfortable first-round progression.
Nadal surged into a 4-1 lead before taking the first set and rounded off his 6-2 6-2 victory by reeling off the last four games in the second.
"This was a very important victory for me. I played a good match, a solid one. I played with not many mistakes," he explained after his first match since losing to Feliciano Lopez in the second round in Shanghai.
"The important goal for me is to try my best in the next round and to enjoy every minute on court and the love of the fans. To enjoy tennis and enjoy the tournament."
After a positive start to his first Basel campaign in 10 years, the second seed will now face Pierre-Hugues Herbert after the Frenchman overcame compatriot Edouard Roger-Vasselin 6-3 6-7 (5-7) 7-6 (7-3).
The 23-year-old qualifier hit 26 aces and saved each of the four break points he faced in a match that lasted over two hours.
Seventh seed David Goffin is also into the next round after he moved past Austria's Dominic Thiem 7-6 (7-4) 6-3.
The Belgian was in fine form on his serve - hitting 15 aces to Thiem's one - as he made it three career wins from three against the world number 39.
Donald Young came out on top against Argentina's Carlos Berlocq, triumphing 7-6 (7-5) 6-4.
Young trailed 3-2 in the first set before recovering to progress on a tie-break.
The American then spurned a 3-1 lead in the second to trail 4-3, before taking three games in a row to secure victory.