Two first half goals had put the Ukrainians in the box seat before the young Lions narrowed affairs midway through the second half through Noni Madueke .
A furious late rally saw Charlie Cresswell head home two minutes to seemingly preserve England’s unbeaten start to Group F.
But deep into injury time Ukraine snatched the most dramatic of wins when Illia Kvasnytsya fired in a stunning shot.
Lewis and McAtee, who is on a season-long loan at Sheffield United, were both deployed in midfield as England sought to make it three wins out of three in Group F.
However, the defending European champions endured a tough night against a talented Ukraine side in a clash played in Slovakia due to the ongoing conflict in Ukraine.
The Lion cubs had made the early running with Jarrad Branthwaite having gone just wide with 16th minute header before Jamie Bynoe-Gittens then saw a goal bound header blocked in the box.
However, it was the Ukrainian youngsters who struck first on the half hour.
A searching cross from the right flank evaded Tino Livramento and Ukrainian forward Nazar Voloshyn despatched a low shot past James Trafford into the corner of the goal.
Noni Madueke sought to get Lee Carsley’s side back into the game as he weaved into the Ukrainian box before sending a low shot just go past the wrong side of the post.
However, a tough night got even harder on 42 minutes when Ukraine doubled their lead with a stunning Oleh Ocheretko free kick from the right side of the box.
It was rifled into the top corner by the midfielder giving Trafford no chance whatsoever.
England sought to up the intensity after the break with Lewis and McAtee at the heart of much of their best work.
Delap – who is on a season-long loan at Preston – was also summoned from the bench to try and help provide more of a cutting edge.
Fellow sub Jaden Philogene lashed a shot wide while Lewis appeared to be brought down in the box – only to be booked for simulation.
But England’s intensive pressure finally brought its reward on 67 minutes when they reduced areas thanks to a superb strike from Madueke after Delap had caused mayhem in the box.
And two minutes from time, Cresswell’s close-range header looked like rescuing a point for Carsley’s side.
But in an incredible denouement, the hosts claimed a dramatic win three minutes into injury time as Illia Kvasnytsya struck a superb shot from the edge of the box to restore Ukraine’s lead.
Even then the drama wasn’t over with a Delap header somehow saved by the Ukraine deep into the sixth minute of stoppage time.
However, Ukraine held firm to make it three wins out of three to lave England in second place.
