Ronaldo, who played under Mourinho for three years at Madrid, announced on Thursday that he had played his final match for Portugal after a world-record 234 appearances and 146 goals.
"It's not a retirement; his career hasn't ended. Anyone who knows him knows he still has goals for his career," Mourinho said ahead of his team's match at Valencia.
"The only thing I would hope for is that when the day finally comes for him to retire as a footballer, it happens differently than it did yesterday."
Ronaldo, a five-time Ballon d'Or winner, fell out with Portugal coach Jorge Jesus at the end of September after he refused to play the forward in a Nations League match.
The 41-year-old immediately left the team camp and was handed a 30-day suspension, a sad end to his international career which included winning Euro 2016.
Ronaldo will continue to play for his current club in Saudi Arabia, Al Nassr, where he is under contract until June 2027.