The top seed took the first set 6-4 on Rod Laver Arena before his Australian opponent withdrew, with the decision appearing not to go down well with some sections of the crowd.
Nadal took the only break point in the set to move into a 5-4 lead and then closed out the set in 39 minutes.
The Spaniard missed last year's tournament with a stomach virus and admitted and admitted his return to Melbourne had been "really emotional".
He said in an on-court interview: "The final against Novak (Djokovic) two years ago, even if I lost (Djokovic won in five sets), is one of the top moments of my career.
"I really enjoy playing here so much in Australia. I am sure I missed you more than you missed me last year."
Nadal will next face another home player, Thanasi Kokkinakis, the 17-year-old world number 570.
And he said he was pleased with his fitness at the start of the year.
"My first goal of last year when I came back was to finish the year, and that's what happened," he added. "I finished the year and I finished the year playing one of the best seasons of my career.
"I am able to start agains this year and that's the best news possible."