The French champions missed their chances and then ran out of steam and ideas after the break, with former youth academy graduate Kingsley Coman, who left the club in 2014 as a free agent to join Juventus, heading the winner just before the hour.
Neymar and Mbappe, recruited for a combined €400 million, did not score in the "Final Eight" tournament in Lisbon despite 23 shots between them. Tuchel, though, refused to blame either of the pair for the defeat.
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"Neymar has had a great tournament, he cannot do everything," the German said.
"Mbappe, it's a miracle that he was with us after sustaining a serious [ankle] injury [in July]."
Marquinhos echoed his coach's sentiments, adding that he was proud of the progress Les Parisiens had made this season.
"We're a team, it's not any individual's fault," Marquinhos said. "We have to be proud of our team.
"Nobody thought we'd do that well in this campaign. We're disappointed because we wanted more but we need to continue like this, to make sacrifices, to work for each other. We have to think about the next campaign and see what we can do better."
"Right now it's difficult to sleep, it's difficult to speak, it's difficult to explain," disappointed midfielder Ander Herrera added.
"But, from tomorrow, at least myself, and I'm sure my teammates as well, we're going to start again. We've built something very, very important for the club."
Tuchel said that the tense final could have gone either way.
"It was a fight. We gave everything, we left our hearts, everything, on the pitch. You can't control the result," he added.
"I had the feeling the first goal would decide the final. I'm disappointed but not too much. We were very, very close.
"What did we need to win? The first goal. If we had scored the first goal we would have won the game with the same scoreline."
Asked if he would still be in charge next season, he said: "I have a contract that's all I can say."