Paraguay international Lucas Barrios scored twice and Kevin Grosskreutz, Mats Hummels and Robert Lewandowski added one apiece to lift Dortmund to 12 points with their fourth straight win, three behind Mainz who beat Cologne 2-0 on Tuesday.
Last season's runners-up Schalke notched their first three points thanks to Dutchman Huntelaar's 86th-minute winner but having lost their first four games they remained bottom of the table.
Dortmund have not dropped a point since their season-opening defeat by Bayer Leverkusen and were in a class of their own against promoted Kaiserslautern.
Barrios opened their account with a well-placed shot before Grosskreutz took the wind out of the visitors' sails with a curled strike from the edge of the area seven minutes before the break.
Coach Juergen Klopp's team could have added a handful of goals before Hummels made it 3-0 with a header just past the hour as the visitors collapsed under their rivals' continuous pressure.
New signing Lewandowski grabbed his second goal in two league games by finishing off a quick break and Barrios tucked in his second two minutes from time.
It was much harder work for struggling Schalke, who took the lead through Ivan Rakitic but failed to build on it.
Sloppy defending, which has cost them dearly so far in the season, allowed the hosts to equalise with Papiss Cisse slotting home from close range in the 69th minute.
With most of their big names, including Spanish striker Raul, struggling in a lacklustre second half, the game looked to be heading for stalemate when Huntelaar sneaked into the box to convert a Joel Matip cross with four minutes left to play.
Freiburg ended the game with 10 men after Ivica Banovic was sent off in stoppage time.