Spurs were knocked out 3-2 on aggregate after Mislav Orsic scored an incredible hat-trick for the Croatian side.
The 28-year-old struck twice in the second half to force the game to extra time and then came up with a glorious solo goal in the 106th minute to send his side into the quarter finals.
Mourinho was no doubt furious with his side's capitulation against a side who had their manager resign after being sent to prison for fraud this week, but the first thing he did was to congratulate the victors.
A video of the Portuguese boss making a beeline for Dinamo and applauding their displays after the game has been shared on social media.
Post-match, Mourinho spoke of his trip to the opposite changing room and pointed out the difference in attitudes from the two sides.
"To say that I feel sad is not enough because what I feel goes much further than sadness," he told BT Sport.
"I just left Dinamo dressing room where I went there to praise the guys, and I feel sorry that one team that is not my team won the game based on attitude, based on compromise.
"So I feel more than sad and that's it. Football is not just about players that think they have more quality than others, the basic of football goes beyond that. The basic of football is the attitude and they beat us on that.
"Many times I fear my thoughts, my feelings but I don't ban myself in a sense I always share them.
"Before the game I told the players the risks of a bad attitude. At half-time, even at 0-0, I told the players the risk of playing the way we were playing.
And it happened, because I believe the players only realised the game was at risk when they scored the second goal and it went to extra-time."
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