Bayern appeared to be running away with the game after goals from Andreas Ottl and Lukas Podolski (two) put them 3-0 up inside 20 minutes.
But the home side responded positively in the second half with Mihai Tararache and Markus Daun narrowing the gap within 10 minutes of the restart.
It was not enough, though, as results elsewhere ensured Duisburg were relegated to the second division after just a year in the top flight.
Despite having the title in the bag, Bayern were clearly taking this game seriously and stunned Duisburg with an early three-goal salvo.
Ottl set the champions on their way in the third minute, taking advantage of a poor clearance from Tararache to drill a low shot from 20 yards into the bottom corner.
Minutes later Tararache almost made up for his error with a decent effort on the Bayern goal but a quickfire brace from Podolski within the space of two minutes seemed to have decided the game in Bayern's favour.
Moments later, Podolski made it three when he lashed home the rebound after Sosa's shot had been saved by the Duisburg goalkeeper.
In the second half, Tararache made amends for his earlier mistake with an excellent strike from 20 yards after 49 minutes before Daun pulled another goal back for the hosts in bizarre fashion.
His shot was blocked by Daniel van Buyten but rebounded back off Daun's standing foot to loop over Oliver Kahn and in to the net.