Mbappe scored twice in the second half as France came back from 4-0 down at half-time, a comeback built on goals from the Real Madrid forward and Bradley Barcola that cut the deficit to 4-3, before England pulled away again through a Bukayo Saka penalty.
Ousmane Dembele pulled another back late on, but Jude Bellingham settled the match for England deep into stoppage time. Mbappe's brace took him to 22 career World Cup goals, one more than Lionel Messi's all-time record, and gave him 10 for the tournament to seal the Golden Boot ahead of the Argentinian.
Speaking after the match, Mbappe reflected on a night that swung wildly between a humiliating first half and a spirited second-half fightback.
"I don't know. There were two different halves," he said. "I understand those who think it's a total farce.
"We didn't respect the shirt. We were human. We can't allow ourselves to be human. They woke us up. We became top-level players again in the second half, mental machines without feeling.
"In the end, we don't win, and that's especially a shame for the coach. It gives the impression that we let him down, and that's not the case at all. We wanted to do something for him, and this isn't what we wanted to do for him. And this match won't tarnish Didier Deschamps' legacy."
The defeat marked the final match of Deschamps' 14-year reign as France manager, and Mbappe made clear his primary disappointment was not being able to send his long-serving coach off with a win, rather than any personal achievement on the night.
Asked about his record-breaking goal tally, Mbappe played down its significance.
"Record? Leo scores all the time, I said it, tomorrow he's going to score for sure," he said. "I'm just trying to help my team and score. Scoring that many goals makes you grow, but I would have preferred not to be the World Cup's top scorer and to be playing tomorrow instead. It's good for the legacy, but it's not the first thing on my mind."
Mbappe's tally means he now sits alone at the top of the all-time World Cup scoring charts, surpassing the mark Messi set across five tournament appearances for Argentina, with the France captain achieving the feat in three World Cups.