The Ligue 1 outfit ensured progression from Group I in top spot after a 2-1 victory over Vitoria Guimaraes at the Estadio D. Afonso Henriques.
However, Lyon were made to work hard for their third victory of the group stage, requiring second-half goals from Bafetimbi Gomis and Jordan Ferri to overturn Tomane's opener.
Garde believes his team can get better in the knockout phase, but declared himself satisfied at Lyon's overall performance in the competition.
"The main thing is to have qualified and won the group (but) not everything is perfect," he said.
"We predicted we'd have a few difficult moments (on Thursday), but the reaction the players showed in the second half was full of character.
"At half-time, I tried to keep the players' confidence high. They needed to take the shackles off."
Lyon return to domestic action on Sunday when they face Marseille at the Stade de Gerland.
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