Son broke his right arm on Sunday in a Premier League win over Aston Villa, and Tottenham initially said the South Korea was expected to miss several weeks.
However, Mourinho was more pessimistic when assessing Son's recovery time.
"I don't count on him again this season," Mourinho said at a news conference ahead of Tottenham's Champions League game against RB Leipzig. "Yesterday (we got) the bad news - the first thing was to break our hearts and the second thing was to break our team. But we have to recover from broken hearts and we have to fight with the team we have."
Son was injured in a first-minute challenge with Villa's Ezri Konsa but still completed the 90 minutes and scored twice.
He will undergo surgery this week, Tottenham said
"Following surgery, our medical staff shall be reviewing management options for Son's rehabilitation with the player expected to be sidelined for a number of weeks," the club said in a statement released hours before Mourinho's news conference.
The injury leaves Tottenham short up front, with first-choice striker Harry Kane also a long-term absentee with a hamstring injury.
Son has been deputizing as the main frontman since Kane's injury but with both players now missing, Lucas Moura or untested youngster Troy Parrott may be required to step in.