Full-back Ben Foden's solo try dragged England back into the contest but Francois Trinh-Duc's drop-goal left the Red Rose side needing two converted tries to win it and all they offered in response was Mark Cueto's late score.
But Johnson, who led England to the 2003 triumph as a player, backed his side to emerge better side from their World Cup heartache.
"This team's best days are ahead of it," he said. "The core of them are very young playing at their first World Cup. But they will be far better as we go into next year.
"In the first half, when we had the ball we looked OK but the thing that really killed us was that when we were under pressure they scored two and they were soft tries.
"The guys were still confident they could do something in the second half. We had to score pretty quickly.
"Ben scored but you have to bounce back with another score and we lost possession. I'm proud of the way they came back but at 16-0 but we gave ourselves too much to do. They scored their tries early and we were chasing."
With the French camp engulfed in a war of words with their own coach, Marc Lievremont, in the build-up to the game, all eyes were on which France side would turn up.
It didn't take long for England to find out it wasn't the rag-tag bunch that had lost to Tonga as Dimitri Yachvilli slotted two penalties and Clerc span through a series of weak tackles to put France 11-0 up.
Medard soon followed his team-mate over the whitewash for France's second try and when Jonny Wilkinson threw the ball over Chris Ashton's head with the try-line begging the writing appeared on the wall.
But on 54 minutes following a tap-and-go penalty, Foden cut through France to allow England to dream of a historic comeback but Trinh-Duc landed three more points to knock the wind out of their sails and render Cueto's unconverted try redundant.
"We let them get their tails up. They have got lots of dangermen and they got a foothold in the game with the points on the board," said fly-half Wilkinson.
"We gave ourselves a massive task, but I'm proud of the way the boys took on that task. This team will stay together, keeping building and I'm sure the next World Cup will be different."