Leroy SanĂ© gave Germany the lead inside two minutes, but NĂslon Angulo levelled with a curling long-range finish in the ninth minute. The game stayed level until the 77th minute, when a MoisĂ©s Caicedo header flicked the ball into the path of Gonzalo Plata, who poked it past Manuel Neuer to send Ecuador through.
Germany finish top of Group E regardless. Ecuador advance in third after the result elsewhere went their way.
Plata, who scored the winner, reflected on what the result meant.
"We were really looking forward to this before the World Cup began," he said. "It feels different today because we struggled so much in the first two matches. It's better this way â it's a learning experience for us, and now we'll go into the next round even more hungry for glory. This team believes strongly in itself. We have 26 players who will give their all for Ecuador."
He expanded on the relief of finally scoring after a goalless start to the tournament.
"We know Germany are destined to be among the candidates to lift the trophy here. It was a very difficult game and thank God we were able to take those two chances. In our two previous games we couldn't do that and find the net. Thankfully the confidence of the group was intact and we could turn the situation around."
Ecuador coach SebastiĂĄn Beccacece kept the moment in perspective.
"It's not about what it means to me â this is for the people. The players have given them this qualification. Let them celebrate and enjoy it."
Germany coach Julian Nagelsmann acknowledged the structural failings that cost his side.
"We have to learn that after a good start and an early lead, we can play with more composure instead of suddenly switching positions too much," he said. "There was too much freestyle. We just need to be more patient and stay a bit more structured in our positions. And if on top of that we're giving the ball away too often, at some point it becomes difficult."
Captain Joshua Kimmich was direct.
"We started well, but then we gave the ball away too cheaply and kept inviting them on. We made it easy for them and let them grow into the game. In the second half, the defeat was deserved."
Striker Deniz Undav drew a clear conclusion.
"Ecuador were more aggressive and sharper than we were. That's something we need to learn from and draw the right conclusions. We weren't as direct in our play and we didn't create as many chances. We have to perform better. But there's no time to dwell on it â we're back in action on Monday already."
Midfielder Pascal Gross placed the defeat in the broader context of a group stage Germany had otherwise dominated.
"I think, all in all, it was a good group stage. We played very well â two good wins in the first two games, and today unfortunately we lost. We'll take a lot of confidence into the knockout phase. Knockout games are totally different from group games. We're daring and we know that on a good day, we're very difficult to beat."
Defender Antonio RĂŒdiger offered the calmest assessment of all: "It's always difficult to lose a game, but in the end we've just lost one game. We're in the next round and now have another game to do better."