Leading 15-10 with just seconds remaining thanks to tries from Ashton Hewitt, Garyn Smith and a penalty and conversion from Angus O'Brien, Wales looked to have the game wrapped up.
But after the full time hooter had sounded, England's Alex Lundberg broke Welsh hearts with a late try, Sam Olver kicking the conversion to seal the win.
England had led 5-0 at half time thanks to a try from James Mitchell.
And although Wales stormed back in the second half, they were denied at the death.
Despite the defeat, Lewis was in positive mood, emphasising how far his side have come in the last six months.
"The boys played exceptionally well," he said.
"When you consider that when we last played England they scored seven tries against us, today shows the improvement we've made.
"England scored two tries against us today, in the first and last minute, but we were superb defensively and every player wore their shirt with a huge amount of pride.
"I can't criticise them at all. This tour is a wonderful developmental opportunity for the boys and they'll learn a huge amount from it."
The game itself had started badly for Wales. The anthems had barely finished before England were ahead, Mitchell diving over in the corner after a mistake by Wales.
The conversion went awry but after an early warning, Lewis' side began to grow into the game. With their kick chase and defensive game impressing, Wales were now creating opportunities though the boot of O'Brien.
Sadly for Wales, the Dragons fly half, who had kicked nine from nine in the win against France, put two penalty efforts wide as Wales remained 5-0 down.
Nonetheless, Wales had begun to show some positive signs, their scrum in particular going well. Indeed, one huge shove from the Wales eight saw them turnover ball from an English put in.
With their pack showing up well, Lewis was forced into a change with Ospreys forward Jon Fox replacing Tom Phillips who suffered an injured shoulder.
There were though, no further first half scores as England went into the break with the advantage.
If Wales had failed to put points on the board in the first half, it didn't take long for them to make amends after the interval.
Hewitt, who had caused France all sorts of trouble in the first game of the tour, added his third try of the trip and with O'Brien successful with the conversion, Wales were now in front.
It soon got even better. Smith, starting on tour for the first time at inside centre, broke through a number of English tacklers to score in the corner.
And although Wales were forced into another change with Ryan Elias replacing the injured Torin Myhill at hooker, it was Lewis' side who were now on top.
Further replacements failed to hinder Wales and with Leon Crump, Javan Sebastian and Adam Beard all entering the fray, Lewis now had fresh legs to call on.
England refused to give up though and with 66 minutes gone, Josh Skelcey dived over to get the men in white back into things.
The score made it 12-10 and although O'Brien looked like he'd won it for Wales with a penalty minutes from the end, there was late heartbreak.
After the full time hooter had gone, England had no option but to tap and run and were rewarded with Lundberg diving over a number of phases later.
And when Olver nailed the conversion with the last kick of the game, Wales were left to stomach a last minute defeat.