Bayern had been unbeaten in 18 matches but goals from Naby Keita and Timo Werner saw Leipzig come from behind to claim the club's first win in this fixture.
Heynckes' men are 17 points clear of nearest rivals Schalke following their defeat, with title celebrations having to wait until after the international break, and the veteran Bayern coach had no arguments about his side's 2-1 loss.
"We faced an excellent opponent today," Heynckes said. "We have to acknowledge that.
"Leipzig were really aggressive and ran hard to press us. We didn't play as well as in recent weeks. Leipzig deserved to win.
"There are always games like today when you're not at your best and don't defend well."
Victory came at a cost for Leipzig, though, with midfielder Marcel Sabitzer suffering an ankle injury during the game.
Regardless, coach Ralph Hasenhuttl was thrilled with his side's performance in beating the champions-elect, particularly before the break.
"A big compliment to my team," Hasenhuttl said, with Leipzig having switched to a three-man defence to take on Bayern.
What an intense Match today, big fight but this time not the result we wanted. Now it's time for a short "break" and i am really looking forward to the games with the @DFB_Team— Mats Hummels (@matshummels) March 18, 2018
"Today we played a new system, which we have trained only once before.
"The start was certainly not optimal, but we pulled it through with a lot of mentality to the end and deserved to win.
"We did not want to let them have a lot of rhythm and we achieved that. I think the first-half performance was one of the best I have ever seen from us."