France's coach, Marc Lièvremont, said that with this astonishing defeat, his team had achieved a "bitter" qualification for the World Cup quarter-finals.
Les Bleus needed a late try from the wing Vincent Clerc to take the losing bonus point they needed for second place in Pool A behind New Zealand and a last-eight date with England. Sukanaivalu Hufanga scored Tonga's try and Kurt Morath kicked 14 points.
"I don't think we can be happy with this qualification," said Lièvremont. "It's a bitter qualification but we have qualified. This week will be very important. We've had two defeats from four matches."
Lièvremont again denied there was any unrest and unhappiness within the French squad, and implored his players to show more fight in the knockout stages.
"I trust my players. I want them to fight better. I want them to be more accurate," he said. "I don't think we need to dwell [on] or analyse the technical aspects of the match now. I want them to react and refocus. We have no choice.
"We're still alive. We'restill part of this adventure and I still want to fight and I think my players still want to fight too, though they are disappointed after tonight's performance."
Despite the evidence of scratchy wins over Japan and Canada and defeats by the All Blacks and Tonga, France's captain, Thierry Dusautoir, said his side could beat England.
"After such a defeat like this the group is really upside down," he said. "If we go on playing like this against England we're going to lose and we'll go straight back to France. The group will have to strengthen itself and this is going to be difficult after today. But we've got nothing to lose because we will be the underdogs. "
Tonga's coach, Isitolo Maka, said he hoped his side's superb win would result in more Tests against tier-one nations. When the Tongans faced New Zealand in the World Cup opener last month it was the first time they had played a major team since the previous tournament, in 2007.
"This win has really helped Tongan rugby and I hope the IRB will give us a Test match against a tier-one country," said Maka, who is a former New Zealand back-rower. "For us to beat France is very special. All the Pacific Island teams have done so well. Samoa did a great job last night against South Africa and while they didn't win it did really help us.
"The win tonight, you people don't know what it means to me and to our people back in Tonga," he added. "In Tonga right now our people are going crazy. We are going to get a lot of support when we get to Auckland tomorrow. I think this World Cup has really come alive."
France M Médard; V Clerc, A Rougerie (F Estebanez, 58), M Mermoz, A Palisson (C Heymans, 75); M Parra (F Trinh-Duc, 58), D Yachvili; JB Poux (F Barcella, 6), W Servat (D Szarzewski, 49), L Ducalcon, P Pape (J Pierre, 66), L Nallet, T Dusautoir (capt), R Lakafia, J Bonnaire.
Tonga V Lilo; V Iongi, S Piutau, A Ma'ilei (A Fatafehi, 61), S Hufanga; K Morath, T Moa; S Tonga'uiha (S Taumalolo, 47), A Lutui, K Pulu (N Aulika, 42), T Lokotui, P Hehea (J Tuineau, 57), S Kalamafoni, S Ma'afu, F Maka (S Vahofolau, 10).
Referee S Walsh (Australia).
Pens: Yachvili 3
Pens: Morath 4