The England captain has recently returned from an ankle injury but despite Mourinho wanting him to travel to Budapest and be part of the squad, he opted to stay in London in order to rest.
Spurs did just fine without him as goals from Son Heung-min, Gareth Bale, Lucas Moura and Carlos Vinicius earned a 4-1 win as they put one foot in the last 16.
Mourinho said Kane was concerned after his recent injury and a hectic schedule, but that his top scorer should be back involved against West Ham on Sunday.
“I believe so, but experienced guy that had injuries in the past, he knows his body better than anyone,” Mourinho said. “He knows that I want him to play every minute of every game, so it’s never a question of a choice.
“I wanted to come here with the best team and the players that could give us more opportunities to win the game and get a good result, but he made the decision based on his feelings.
“His feelings were that to play this game could be a risk with the accumulation of minutes and the accumulation of minutes after the injury that he had.
“Of course myself and the medical department, we agreed with him in giving him this opportunity to take care of his condition, but I believe on Sunday he will be OK and ready.”
It is the second time in a week that Mourinho has had to deal with a player telling him he did not want to play after Bale did similar for last week’s FA Cup tie at Everton.
That was a new nadir for the Wales international in what has been a disappointing return to Spurs, but his last two outings have suggested there may still be life in him yet.
After an impressive cameo in the 3-0 defeat at Manchester City on Saturday, he put in his best performance of the season against the Austrian side, assisting Son’s early opener and then scoring a fine goal to double Spurs’ lead.
Bale was taken off midway through the second half and Mourinho has hinted he too could be involved against the Hammers on Sunday lunchtime.
“One of the reasons why he left the pitch by minute 65 was to try to have him available for the next match because one of the things that is not easy related to his condition is the accumulation of minutes,” the Portuguese added.
“So by taking him off at that minute we managed to save him a few miles in his legs and probably, I know the match is Sunday at 12pm, but I believe he has a chance to play the match.
“Let’s wait, he is the kind of player that his experience, his feelings is a very important thing, like Harry Kane, we have to trust these players and their knowledge of their body and their feelings. I believe for him it was important for him to play but not play the 90 minutes.”
Moura made it 3-0 at half-time and after Wolfsberger – the lowest-ranked team left in the competition – got back in it through Michael Liendl’s penalty Vinicius grabbed a late fourth, which left Mourinho admitting his side were as good as through.
“Pleased with the result because of course 4-1 away from home gives you a good space for any possible mistake that you can make in the second leg,” he said.
“I think we have one foot in the next round. The result is of course very good.”
