Bayern, who are not in action next week, have gone the whole year without a league defeat with their last loss in the Bundesliga dating back to October 2012.
They clinched their 19th unofficial "autumn championship" at the season's halfway mark.
Second-placed Bayer Leverkusen, in action on Sunday, can cut Bayern's lead back to four points with one game left in the Bundesliga before a break until January.
With Franck Ribery and David Alaba on the bench and Arjen Robben injured, Bayern were initially made to work hard against battling Hamburg, eager to redeem themselves for last season's 9-2 demolition by Bayern.
Mario Mandzukic struck at the right time when he nodded in after 42 minutes. Mario Goetze's superb control and volley seven minutes after the restart gave them a two-goal cushion before Xherdan Shaqiri killed off the game in stoppage time.
Hamburg had briefly cut the deficit in the 87th minute through Pierre-Michel Lasogga.
Borussia Dortmund battled back from two goals down to draw 2-2 against Hoffenheim but dropped further points after having won one of their last five games to stay in third place.
Goals from Sven Schipplock and Kevin Volland put the hosts in the driving seat in the first half but a goalkeeper fumble before the break saw Dortmund cut the lead though Pierre-Emerick Aubameyang. Lukasz Piszczek levelled from close range in the 67th minute.
Despite frantic attacking by Dortmund and hitting the woodwork the visitors could not find a third goal to complete their comeback, meaning they dropped five points behind Leverkusen and 12 behind Bayern.
Borussia Moenchengladbach failed to take advantage of Dortmund's slip-up when they drew 0-0 at Mainz 05 to see their six-game winning streak snap and stay on 32 points along with Dortmund.
Nueremberg looked set to notch their first league win of the season when they led 3-1 at Hanover 96 before a double strike by Senegal's Mame Diouf in the final minutes rescued an unexpected 3-3 draw for the hosts.
(Reporting by Karolos Grohmann; editing by Martyn Herman and Josh Reich)
