Leipzig were high on confidence heading into the game after six consecutive wins and they got off to a great start as Naby Keita opened the scoring with a stunning strike after just two minutes thanks to an assist from Marcel Sabitzer.
The hosts were responded, though, Florian Niederlechner levelling the scores in the 15th minute after being set up by Pascal Stenzel.
Promising youngster Werner, 20, then showed what he is made of as he restored RB Leipzig's lead part-way through the first half, before making it 3-1 with his seventh league goal of the season in the 35th minute.
Freiburg came close to pulling one back when Nicolas Hofler hit the woodwork on the hour mark, but Sabitzer ended their hopes of salvaging a draw when he netted the 4-1 in the 79th minute.
Misfiring Bayern can narrow the gap to three points again with a win over Bayer Leverkusen on Saturday.