The visitors, who are competing at this level for the first time, went into Tuesday's game as surprise pacesetters following an unbeaten start to the campaign, but were brought back down to earth with a bang.
Mario Gotze enjoyed a double strike for the champions, while the under-fire Robert Lewandowski netted for the second time this term and Thomas Muller completed the scoring in the latter stages.
Bayern had also trailed Mainz and Hoffenheim on goal difference prior to the Paderborn clash, but are now clear at the summit after that pair both dropped points.
Mainz looked in control of their game at Frankfurt after first-half strikes by Jonas Hofmann and Shinji Okazaki, but Alexander Meier pulled one back just before the break and Haris Seferovic equalised late on for the hosts to make it 2-2.
Hoffenheim also had to settle for a share of the spoils following a six-goal thriller against Freiburg at Rhein-Neckar Arena.
Mike Frantz bagged a brace after 31 and 33 minutes to stun the home fans, but Tarik Elyounoussi replied on the stroke of half-time and then Sebastian Rudy levelled things up just after the hour mark.
Vladimir Darida edged Freiburg back in front from the penalty spot, but then went from hero to villain when shown a red card with 10 minutes left to play and Hoffenheim finally made the man advantage count when Jannik Vestergaard made it 3-3 in stoppage time.
Schalke had picked up only two points from their first four fixtures before visiting Werder Bremen, but Jens Keller's side hit form in emphatic fashion with a 3-0 success at the Weserstadion.
Max Meyer put the away team in front just after half-time, Roman Neustadter added a second three minutes later and Tranquillo Barnetta wrapped things up late on.
