Paul Fairclough’s Three Lions went down to a 2-0 defeat and it was heartache with both goals coming in the game’s closing stages.
There were plenty of National League players on show, with new AFC Fylde signing Kurt Willoughby and Hartlepool’s new keeper Ben Killip chosen after a busy summer for them.
England arguably deserved more in Tallinn, but couldn’t make the most of their chances.
They were punished for that in the closing stages of a tight match as Estonia came on strong late in the game.
Markus Poom, the son of former Derby goalkeeper Mart, put the hosts ahead with two minutes left on the clock.
It was all over for England in the last few moments when substitute Kaarel Usta put the finishing touches on the victory.
England C line-up:
Ben Killip, Luke Trotman, David Longe-King, Mitch Dickenson, Alex Brown; Ryan Croasdale, Tom White; James Hardy, Ephron Mason-Clark, Kurt Willoughby, Joe Rowley
Subs: Ryan Huddart (Killip) Isaac Galliford (James Hardy) Wes Fonguck (Rowley) Matt Lowe (Mason-Clark)