Timo Werner's penalty proved to be the difference as Tottenham Hotspur found it difficult to hit the back of the net without Harry Kane and Son Heung-min.
Estonia vs Germany: Ilkay Gundogan struck twice before replacement striker Timo Werner added a third to keep Germany on course to qualify for Euro 2020.
The draw against Germany was enough to send the Netherlands into the Nations League knockout stages as Group One winners.
Mexico created the first upset of the 2018 FIFA World Cup, overcoming defending champions Germany 1-0 in a frenetic Group F game at the Luzhniki Stadium on Sunday.
FIFA World Cup 2018, Highlights Germany vs Mexico: Mexico beat defending champions Germany 1-0.
Timo Werner was in the thick of the action for the 62 minutes he played during the Germany vs Saudi Arabia FIFA World Cup friendly.
World champions Germany will face Chile in Sunday's final in St Petersburg while Mexico play Portugal in Moscow's third-place play-off