Despite the win, his fourth title of the season, Bayern Munich's Pep Guardiola says he has endured the toughest year of his coaching career.
Guardiola finishes his first season in charge of Bayern with four trophies having already won the Bundesliga title, Club World Cup and UEFA Super Cup.
Having arrived in Bavaria with a glowing reputation after winning 14 titles in four seasons at Barcelona, Guardiola says the current campaign has been tough.
"It's my fifth year as a coach and it's been the hardest year of my career," said Guardiola.
"My German isn't so good and coming in after (predecessor) Jupp Heynckes won the treble, wasn't easy for me.
"Each trainer has his own ideas and I know the players were thinking, 'why do we have to make changes?'"
Bayern lifted the German Cup for a record 17th time to claim the domestic league and cup double and the Champions League was the only title to elude them this season.
But Guardiola admitted he deserved criticism from the German media in the wake of their 4-0 home drubbing by Real Madrid in the Champions League semi-final, second-leg, and says Bayern must improve.
"The criticism was quite justified, I did things I shouldn't have done," said Guardiola.
"I made mistakes in our playing style and tactics against Real, but things like that can happen in big games against big clubs.
"Now I know a bit more about German football, you have to win everything here, but even when you do, it's still not enough. I am happy, but we have to improve."
Having also scored the late winner in the 2013 Champions League final against Borussia at Wembley, Netherlands winger Robben again broke Dortmund hearts before Müller's late second.
"We were finished at the end," admitted Dortmund's coach Jürgen Klopp who was left fuming after television replays showed a second-half Mats Hummels header crossed the goal-line, but was not given.
"We tortured ourselves and gave everything. In the phase when we were stronger, we scored a goal, which wasn't given.
"That should have been seen (by the referee) even without goal-line technology."
Germany head coach Joachim Löw was a relieved man after his captain Philipp Lahm and goalkeeper Manuel Neuer picked up only minor knocks less than a month before the World Cup in Brazil.
"Lahm had a knock on the fibula, which was painful, but the team doctor is convinced it won't be a problem for the World Cup," said Bayern's media director Markus Hörwick.
"Manuel Neuer has a shoulder injury, but it shouldn't be a problem."
There was no fairytale finish for Poland striker Robert Lewandowski who had promised to finish his four years at Dortmund by lifting the cup before joining Bayern next season.
This was the fourth and final time Germany's top two sides met this season with both teams finishing with two wins a piece.
"It is great to have won the double," said Lahm. "You can't always repeat a treble season.
"We have had to take a lot of criticism in the last few weeks, some of it justified, some of it not."