Spurs went into the second leg of the last-16 affair with a 2-0 advantage from the opening fixture, but they surrendered two goals in normal time before Mislav Orsic rounded off his superb hat-trick for the hosts in the 106th minute.
"I am disappointed for a difference of attitude between one team and another," Mourinho told BT Sport after the 3-2 aggregate defeat, adding, "I feel sorry that my team is the team that didn't bring to the game, not just the basics of football, (but) I believe the basics of life, which is to respect our jobs and to give everything."
Mourinho stressed the importance of the occasion to him and questioned whether some members of his squad got complacent as the club tried to reach the quarterfinals.
Despite his fury at his own team, Mourinho said he congratulated the Dinamo players in their dressing room after the game.
"They left everything there. They left sweat, they left energy, they left blood. In the end of the game, they left even tears of happiness. They were very humble, very committed. I have to praise them," Mourinho said.
Tottenham's season is unraveling. There is still an opportunity for the club to win its first trophy since 2008 in April's League Cup final, but their opponents in that encounter are Pep Guardiola's much-fancied Manchester City side. In the two other competitions on offer this term, Everton dumped Spurs from the FA Cup fifth round in February, and Tottenham currently sit a disappointing eighth place in the Premier League table.
There is a widening six-point chasm between Spurs and England's four qualification places for the 2021-22 Champions League campaign.
"I can only apologize to the Tottenham supporters. I hope they feel the same way I feel. Today is live or die - and in this moment, we die," he said.