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.
GEAR:Bundesliga shirts up for grabs here. Save 10% when ordering with Kitbag
"If we said before the season that at this stage we would have 12 points we would have said: yeah right," said Dortmund coach Jurgen Klopp.
"Twelve points are a dream that the team deserves but worked hard to get."
Last season's runners-up Schalke 04 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.
Brazilian Grafite scored twice as visitors VfL Wolfsburg defeated Hamburg SV 3-1 to move into 11th place on six points.
Champions Bayern Munich are in eighth spot following their last-gasp 2-1 victory at third-placed Hoffenheim on Tuesday.
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.
DOMINANT DORTMUND
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.
"This win is a relief," said Schalke coach Felix Magath, who had been under mounting pressure after spending big during the transfer period.
"We were under pressure. I am satisfied with my team though you could still sense their insecurity."
