The world number two Serb advanced after winning the first set 6-4, when his Spanish opponent could not go on with a lower back injury.
"He told me it started yesterday," the 23-time Grand Slam singles champion said. "Hopefully he will be ready for New York (US Open).
"This is never the way you want to win, the crowd was expecting a match, a battle," the 36-year-old added.
"I have mixed emotions with how the match ended. I'm hoping to build form and progress through the tournament by raising my level."
Djokovic is playing in the United States for the first time since 2021.
He was barred from entering the country during the latter stages of the COVID-19 pandemic after refusing to get vaccinated.
Djokovic's next opponent on Thursday will be Gael Monfils, who continued his run of comeback form by defeating Australian Alex de Minaur 7-5, 6-4 to reach a third round for the second consecutive week.
The 36-year-old Frenchman excelled as he beat the weekend finalist in Toronto in two hours with 29 winners to 14 for de Minaur.
"It will be a battle of the veterans," Djokovic said of the over-35 clash.
"Gael is an amazing guy, i truly respect and like him - he brings so much joy to fans.
"He's the most charismatic player we've had in the last two decades."
