After a 1-1 draw at Stadio Artemio Franchi in the first leg, goals from Ryan Mason and Erik Lamela, along with an own from Gonzalo Rodriguez, gave Spurs a 4-1 aggregate victory that put paid to Fiorentina's hopes of European silverware for another season.
The tie remained level before Mason's 25th minute goal at White Hart Lane, but Sousa felt his side were not allowed back into the contest after Lamela doubled the lead on 63 minutes.
He told reporters: "Until 1-0 we were in the game. We knew that this was an important team with great quality, which can withstand high intensity throughout the game.
"After the second goal there was great leadership on their part.
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"The boys gave their all against an important team, who I feel at this time to be among the best five in Europe in terms of intensity, technique and tactics.
"We wanted to go on, but unfortunately it was not possible. After 2-0 we fell away. We struggled."
Fiorentina face a difficult game against Napoli in their next Serie A fixture, and Sousa lamented the short time available for his players to recover.
He said: "It's important to recover as soon as possible. We have a trip that does not allow us to recover in a certain way, but we have to play a game against a team of the highest level in Napoli."