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.
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.
