If anyone was going to score it was likely to be him.
Lewandowski capitalises on a through-ball-gone-wrong which ricochets his way.
He smashes an effort past Weidenfeller and finally Bayern have found the net.
Will the floodgates open?
Bayern;s Mehdi Benatia, top, and Dortmund's goalkeeper Roman Weidenfeller, left, challenge for the ball
70mins: Ribery ON, Gotze OFF
Gotze has been quiet against his former club and he has been taken off.
Ribery has been called upon.
68mins: Alaba wastes a free-kick
It would need to be something special to beat Weidenfeller from 30 yards, but Alaba's free-kick doesn't even test him.
He smashes the effort high and wide and Guardiola is looking to make his first change.
Munich's Arjen Robben reacts to missing a great chance
64mins: Benatia nods wide from four yards!
It is certainly turning into one of those days for Bayern.
The home side whip in a corner and it is half-cleared to Boateng who picks it up on the right-hand side of the box.
He curls a ball in and Benatia rises, unmarked, four yards out and nods the ball just wide of the post.
How did he not score??
60mins: Kagawa nearly doubles Dortmund's lead!
Dortmund have their first chance of the second-half and Kagawa is extremely unlucky not to have doubled their lead.
He receives the ball on the edge of the area, turns and curls a shot just past the right-hand post with Neuer beaten.
Warning shot for Bayern - they could get picked off on the break.
Dortmund's striker Marco Reus (left) celebrates scoring with his team-mates
58mins: Dortmund win a free-kick to relieve pressure
It has been all Bayern in this second-half and Dortmund are relieved they now can take their time over a free-kick.
Mkhitaryan is fouled in the middle of the park.
55mins: Bayern are being extremely wasteful
Guardiola is getting increasingly frustrated with his side's wastefulness.
Boateng plays a wonderful ball to set Muller clean through and his effort is blocked by Subotic.
Lewandowski is screaming at him as he wanted the ball played square.
Shinji Kagawa of Borussia Dortmund and David Alaba of Bayern battle for the ball
51mins: The goal just will not come for the home side
Is it going to be one of those days for Bayern?
Bernat whips a ball in and Lewandowski is completely free in the area.
The Pole has a golden chance against his former side but Weidenfeller stays big and manages to push it around the post.
47mins: Bayern have come out the blocks and look hungry for goals
Well it certainly appears Guardiola has put a rocket up his Bayern players.
The passing is crisper, sharper and with more intent and already both Alonso and Robben have had chances.
Alonso hits one from distance which Weidenfeller gathers easily before Robben curls a shot low and straight at the Dortmund keeper.
Arjen Robben (right) of Bayern smashes an effort into the side netting
SECOND-HALF: Borussia Dortmund get us back underway
The second-half begins with Dortmund leading Bayern 1-0 at the Allianz.
Substitution from Klopp as Subotic is ON and Hummels is OFF. Can only assume that is an injury which is a blow to Dortmund.
SOME OF THE BEST PICTURES FROM THE FIRST-HALF
HALF-TIME: BAYERN MUNICH 0-1 BORUSSIA DORTMUND
Bayern have certainly have more chances but they find themselves behind at half-time.
Klopp's men have counter-attacked superbly and, with Bayern wasting their opportunities, they have capitalised.
ONE MINUTE OF ADDED TIME
Dortmund's Marco Reus (right) scores his side's opening goal
43mins: Dortmund's style is perfectly suited to playing Bayern
Don't get me wrong, the visitors have certainly ridden their luck at times, but they know how to play against Bayern.
They are struggling in the bottom three of the Bundesliga and have lost four league games in a row for the first time in 15 years but their counter attacking is brilliant against a side who dominates possession like Bayern.
Dortmund's Marco Reus (third right) celebrates with team-mates after scoring
40mins: Robben does brilliantly but just cannot score!
That is beautiful football but Robben has to score.
Muller threads the ball into Robben and he shimmies inside and out, taking Weidenfeller out of the game, but he curls a shot into the side netting.
Lewandowski is furious with him.
38mins: Muller is denied!
I am really not sure how Bayern have not found the net in this game yet.
Robben cuts open the Dortmund defence with a wonderful through-ball to Muller.
Muller prods a shot goalwards but the on-rushing Weidenfeller is able to stay big and deny him.
Marco Reus of Borussia Dortmund celebrates scoring the first goal
36mins: YELLOW CARD (Alonso)
Alonso goes in a little late on Mkhitaryan in the centre of the park and takes him out.
An obvious booking follows and he is the first player from either side to be carded.
34mins: Bayern have suddenly stepped up the intensity
It is the first goal Bayern have conceded in the first half of a Bundesliga game all season and suddenly they begin peppering the Dortmund goal.
Muller's looped header forces Weidenfeller to flap the ball away before Bernat smashes a shot across the face of goal.