The defending champions, held by Hertha Berlin in their last outing, are now 20 points clear of the chasing pack as they close in on a sixth successive title.
Bayern were able to put that rare Allianz Stadium stalemate from a week ago behind them by hitting four past Freiburg, who had lost just one of their last 12 matches heading into this clash.
Victory may have been straightforward for the visitors come full time, but they had to survive a big scare early on as Sven Ulreich was needed to produce a big stop nine minutes in to deny Lucas Holer from a one-on-one position.
Freiburg were unable to build on their positive start, though, as Bayern edged ahead in a bizarre manner a little over a quarter of the way through after Thomas Muller's cross hit Alexander Schwolow and ended up in the back of the net.
The second followed moments later, this time through a superb individual strike from Corentin Tolisso, who was able to pick out the top corner from all of 35 yards out.
Bayern wrapped up the points less than 10 minutes after the restart, however, with Wagner this time tucking home a loose ball following some neat interplay between Muller and Juan Bernat.
Muller was involved in the Bavarians' next attacking move, keeping the ball in play and picking out Bernat to head the ball wide at the back post.
The Germany international rounded off the scoring with a smart near-post finish once picked out by Joshua Kimmich from the corner, ensuring that Bayern returned to winning ways in style.
FREIBURG (4-4-2): Schwolow; Stenzel, Gulde, Soyuncu, Gunter; Holer (Ravet 57'), Abrashi (Hofler 45'), Koch, Lienhart (Kath 45'); Haberer, Petersen
BAYERN MUNICH (4-2-3-1): Ulreich; Kimmich, Boateng, Hummels, Alaba; Tolisso, Vidal (Sule 83'); Muller (Rafinha 80'), Thiago (Rudy 74'), Bernat; Wagner