The North London club needed penalties to get past the Bavarians, but Paulo Gazzaniga's save from Jerome Boating ensured that Tottenham Hotspur would be lifting the trophy.
Goals from Erik Lamela and Christian Eriksen gave Spurs a commanding 2-0 lead, before former Spurs transfer target Jan Fiete Arp - who's idol is Harry Kane, pulled one back, and late on Alphonso Davies completed the comeback with a fantastic 25-yard effort.
A missed penalty from Eriksen after David Alaba's spot-kick was saved by Gazzaniga, put Spurs under pressure, however, the Argentinian goalkeeper showed nerves of steel and denied Boateng to win the tournament.
So what can Spurs boss Mauricio Pochettino, the squad and the fans take from the Audi Cup?
Spurs back and fitter than ever
We all know how much physical endurance Pochettino likes to put his players under; this year it has clearly worked.
Both Real Madrid and Bayern Munich were subjected to heavy pressure from the Spurs forwards and midfield, with players like Kane, Dele Alli and Lamela who all struggled with injury and fitness issues last season, leading the press.
Kane said before the Bayern Munich game that he will be able to 'feel the benefits' after an extended break and 'proper pre-season'.
Troy Parrott and Lucas Moura capable of playing up-front when needed
It looks like Fernando Llorente will not have his contract renewed as young Irish striker Troy Parrott continued his good form from the International Champions Cup matches into the Audi Cup.
The 17-year-old striker almost found the back of the net in his cameo appearance against Real Madrid, dragging his shot just a little, hitting the post.
Brazilian forward and hero of Amsterdam Lucas Moura also showed that he can fill in up front when called upon. The former PSG winger almost found the back of the net in the opening minutes against Bayern, with a header which required a brilliant save from Manuel Neuer.
It finally looks like Spurs have good enough back-ups for Kane and satisfactory squad depth up front.
Erik Lamela's mission to impress
Many thought Lamela would be moved on to another club this summer. However, it is clear he has his manager's backing.
The Argentinian attacking midfielder has scored two goals in four games this pre-season and he opened the scoring against Bayern with a perfectly timed run to turn home Georges-Kevin N'Koudou's low cross.
He also put in a stellar performance against Real Madrid, catching the eye with his direct running and link-up play.
It's been six years since Lamela signed and the former AS Roma player still has not lived up to expectation. Maybe this is the year for the 27-year-old?
Forgotten man N'Koudou to get his chance
It was a shock to many when Tottenham announced their squad list for the Audi Cup - as N'Koudou was travelling with them.
The Frenchman has been made available for transfer this summer after making only one appearance for Spurs last season - despite grabbing the assist for Harry Winks' winner against Fulham.
However, the 24-year-old winger looked a new man against Bayern Munich - having been given a rare start in Tottenham colours. He repaid Pochettino's faith in him by skipping past his man before delivering an inch-perfect low cross to Lamela for the opening goal.
Tottenham fans were so impressed by his performance there were calls for him to be given more chances in the team.
Christian Eriksen and Danny Rose set to stay
Following Real Madrid's end of interest in Danish playmaker Christian Eriksen, different reports have suggested that he may be willing to discuss terms for a new contract.
The 27-year-old Dane showed no sign of unsettledness or discontent in Spurs colours - even getting himself on the scoresheet against Bayern with a cool finish into the bottom corner.
Eriksen was joined on the pitch by England international Danny Rose, who is reportedly a wanted man - drawing interest from the likes of Juventus.
However, the 29-year-old left-back put in a calm and collected performance in both games of the Audi Cup.
Rose is a fan favourite at White Hart Lane and it is clear that he is someone who they do not want to be rid of.
Tottenham's next game is at home to Inter Milan in their final pre-season friendly on Saturday 3rd July at 3pm (BST).