Lievremont's men did find themselves 6-3 up thanks to two Dimitri Yachvili penalties but Tonga went ahead courtesy of Sukanaivalu Hufanga's converted try.
Yachvili and Kurt Morath exchanged penalties before the latter added two more, only for Clerc's late try to ensure France advance in second place and book a quarter-final with England.
But Lievremont was far from a happy man.
"I don't think we can be happy with this qualification," he said. "It's a bitter qualification but we have qualified.
"I trust my players. I want them to fight better. I want them to be more accurate.
"I don't think we need to dwell or analyse the technical aspects of the match now. I want them to react and refocus on those values I've already talked about.
"We have no choice. We're still alive. We're still part of this adventure and I still want to fight and I think my players still want to fight too even though they are disappointed after tonight's performance."