The French champions played almost all of the second half with 10 men after Marco Verratti's dismissal but secured qualification thanks to goals from Zlatan Ibrahimovic and Edinson Cavani.
Motta believes his side showed 'heart' to fight on with 10 men and secure the three points through Cavani's 90th-minute strike.
"We managed to get the result and also the berth in the last 16," the Italian midfielder said.
"We played with all our qualities. We also won with our heart, which is important. Winning with 10 players on the pitch is not easy."
Motta also paid tribute to goalkeeper Salvatore Sirigu, who was in fine form to deny the Greek side on a number of occasions, with Olympiakos having levelled through Konstantinos Manolas 10 minutes from time.
"We were much better (than Olympiakos) tonight, especially in the first half," Motta added.
"It was complicated after the break but in the end we had a great goalkeeper."
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