The Scottish champions had already won Group E to secure a last-32 spot before the final fixture in Romania and Lennon made nine changes to the side which beat Rangers 1-0 in the Betfred Cup final at Hampden Park on Sunday.
Lennon left a clutch of key players in Glasgow with 18-year-old midfielder Scott Robertson making his debut.
But after four wins and a draw in the section, the visitors went down to second-half goals from defender Andrei Burca and midfielder Damjan Djokovic to secure second spot for Dan Petrescu's side.
Lennon said: "Obviously I'm disappointed to lose the game but in the main very pleased with what I got out of the game.
"I'm happy to have used the squad tonight because we have so many important domestic games coming up.
"Some players needed the games and needed the 90 minutes.
"My only criticism is I thought we were very passive at the start of the second half and I'm disappointed to lose a goal from a set play.
"But overall we've had an amazing campaign. The campaign wasn't about tonight. The campaign for us was done and dusted and we've already won a trophy so I didn't want to risk injury.
"I wanted to give others some experience and game time and they'll need that for the games coming up.
"I thought (Olivier) Ntcham was unbelievable, to give him the captaincy and to take on the responsibility the way he did.
"I thought he was top class. I was pleased for Craig Gordon as well, he made some important saves."
Celtic's 16-year-old attacker Karamoko Dembele replaced Mikey Johnston in the second half to become the youngest ever player for the club in a European competition.
Lennon said: "That wasn't at the forefront of my mind. We think very highly of him. I wanted to give him some experience. I want to keep him around the squad because he's a real talent."