Bayern set a new points record for the Bundesliga, bettering the 81 managed by Borussia Dortmund last season thanks to Xherdan Shaqiri's single goal in a tight encounter.
"I had warned my team before the game about Freiburg," said Heynckes.
"What (coach Christian) Streich has achieved at Freiburg is sensational.
Something has grown there over the years and it was a really tough game for us today.
"But compliments also to my lads. We played very cleverly and professionally."
Heynckes changed 10 of his players from the side which started against Barcelona on Tuesday with only Jerome Boateng keeping his place, but even with a seemingly weakened side Bayern are in a league of their own, according to Streich.
"We had to play more defensively than ever before today, but there was no other way," he said.
"Bayern are so versatile that you can't play them in any other way. Of course Bayern fully deserved their win."