The Frenchman scored twice as an own goal, a Daniel Van Buyten header and strikes from Mario Mandzukic, Thomas Muller and Mario Gotze left the hosts feeling battered and bruised
Bayern's 11th successive win in all competitions – which helped extend their league unbeaten run to 40 matches – was set up in the first half as Pep Guardiola's men silenced the Weserstadion crowd.
Playing his first match since cracking a rib for France on international duty last month, Franck Ribery helped Bayern into the lead after 21 minutes when his cross was deflected in by Werder defender Assani Lukimya-Mulongoti.
A towering Daniel Van Buyten header doubled their advantage six minutes later before the influential Ribery sealed the result with a composed finish before half-time.
And Mario Mandzukic wrapped up the rout on the hour-mark as Bayern's latest win confirmed they would finish the year at the top of the league, before Thomas Muller, Ribery and Mario Gotze added more polish to the scoreline with late goals.
Ribery, Van Buyten and Muller came in to the Bayern side that beat Augsburg 2-0 in the DFB-Pokal on Wednesday, with Arjen Robben (knee) among the absentees.
There was no sign of captain Philipp Lahm, who continues his recovery from a thigh injury, but it mattered little as the Bavarian giants started brightly.
Mandzukic had an offside goal chalked off in the fourth minute and just seconds later Werder goalkeeper Raphael Wolf had to come off his line to deny Gotze.
Eljero Elia shot straight at Neuer at the other end after cutting in from the right, while Aaron Hunt had a fierce left-footed effort deflected wide by Jerome Boateng after more good work from Elia.
That was as close as Werder got to opening the scoring though, as Ribery beat Clemens Fritz and got to the byline before his ball was turned in by Lukimya-Mulongoti.
Van Buyten then rose above Nils Petersen to head home Toni Kroos' clever free-kick and although Ribery and Mandzukic missed chances to score a third, a break down the right led to another Bayern goal.
Released in time and space, Muller centred for Ribery, who took a touch before calmly slotting past Wolf in the 38th minute.
Neuer saved well to deny Hunt just before the break and his opposite number, Wolf, did superbly to keep out Gotze and Mandzukic after half-time.
Mandzukic got Bayern's fourth, though, stabbing home at the far post after another superb Ribery ball, and Muller then scored with a shot on the turn eight minutes later.
There was still time for Ribery to cap a fine performance as he converted a clever David Alaba cut-back in the 83rd minute, with Gotze netting the seventh with a late close-range finish.