Robert Lewandowski's brace and one apiece from Mats Hummels, Javi Martinez and Serge Gnabry earned the Bavarians a resounding Klassiker triumph on Saturday and sent them hurtling back into top spot with six games to go.
Bayern were brilliant in a four-goal first half at Allianz Arena that blew away the visitors and set up a 14th win in 16 league matches.
Kovac applauded his side's sparkling showing in what could prove a decisive result in the club's bid to be crowned champions for the seventh straight season.
"I think we turned in a top performance, a great performance over 90 minutes," Kovac said.
"The first half in particular was sensationally good in every respect. The way we played was very impressive.
"I'm glad, and I'd like to congratulate my team on it. The margin of victory was completely deserved.
"We still have six matches to go, and you have seen how fast it can change in the league. Very, very difficult matches are awaiting both Dortmund and us, so we won't say everything's decided."
Bayern captain Manuel Neuer was barely troubled in his first match back from a calf injury as Dortmund mustered a lone shot on target.
The goalkeeper labelled the victory a breakthrough moment in a campaign that has taken time to get going.
"We were very dominant," Neuer said. "It was a good team display, and I'm very, very glad about it.
"It was the first big-point match we've won. We had to wait for it for a long time.
"We played well in every position, up front, at the back, and most importantly we worked together."