The visitors twice led through goals in either half from Mathis Bolly and Andreas Lambertz, only for Thomas Müller and Franck Ribery to haul the record champions level on each occasion. Boateng's late header, his first goal in 130 Bundesliga appearances, eventually won it for the hosts, who extend their 100 per cent start in 2013 to eight matches.
He shoots, he scores
Fortuna boss Norbert Meier had said before the game that it was simply a pleasure to take a side who had been in the fourth tier just a decade ago to the Allianz Arena, but the promoted outfit were certainly not overawed by the occasion. Bayern may have dominated possession as per usual early on, yet it was the visitors who took a shock lead after 16 minutes when Bolly prodded Lambertz's header across the line with his first ever shot in the Bundesliga.
Bayern, minus defender Dante from the start for the first time this season, were affronted by their opponents' opener and soon sought an equaliser, but the Fortuna defence stood firm. Mario Mandzukic's header was repelled superbly by Fabian Giefer, who was nevertheless grateful to see Müller blaze over the rebound before Toni Kroos slid another chance inches wide.
Chances by the bucketful
After Mandzukic shinned wide with the goal at his mercy, pair of Giefer parries to deny Daniel van Buyten, not to mention a disallowed Bastian Schweinsteiger finish, it seemed like Bayern's luck may have deserted them. However, parity was rightfully restored on the stroke of half-time as Philipp Lahm controlled deftly on the right before sliding the ball through for Müller to notch his 12th Bundesliga goal of the season.
The second period brought much of the same, with Bayern creating one chance after another but lacking the precision to finish them off. Mandzukic headed over from a Toni Kroos chip before Ribery fizzed a tempter across the face of goal. Müller then headed narrowly wide with Giefer beaten and Mario Gomez, introduced moments earlier for Mandzukic, saw his first touch of the ball diverted behind by the Fortuna keeper.
It therefore came as even more of a surprise than the opener when Düsseldorf retook the lead on 71 minutes, clearing upfield to release captain Lambertz, who raced through to score his first ever Bundesliga goal to the delight of the visiting contingent. The lead lasted but a couple of minutes this time, however, as Ribery combined well with substitute Claudio Pizarro before finishing into the top corner to equalise.
Again chances went begging for the hosts as Gomez glanced onto the bar and Ribery saw his finish kept out by the brilliant Giefer when clean through, but the Bavarians were not to be denied what was ultimately a deserved three points as Boateng rose to head in Lahm's pinpoint centre - the skipper's ninth assist of the season - four minutes from the end.
Line-ups and statistics
Andy James reporting from Munich