Mario Gomez netted the game's opener before Slovakia fought back with two goals before the break, finally sealing victory through Juraj Kucka seven minutes after the interval
Germany goalkeeper Marc-Andre ter Stegen lamented his "unlucky" error in the side's 3-1 friendly defeat to Slovakia on Sunday.
Mario Gomez put the hosts in the lead at the WWK Arena in Augsburg via the penalty spot but Slovakia hit back just before the half-time break.
Napoli's Marek Hamsik found an equaliser in the 41st minute before Michal Duris put the visitors in front, but the costly error came for Slovakia's third goal in the 52nd minute.