The outgoing FCB boss acknowledged the resilience of his side's opponents after digging deep for all three points at the Allianz Arena on Saturday
The Bavarians - who made 10 changes from their Champions League semi-final victory over Barcelona on Tuesday - set a new record points tally of 85 in the Bundesliga thanks to Emre Can's sole strike.
And the 67-year-old revealed that he approached the match cautiously, as he praised opposite number Christian Streich for his "sensational" work in establishling the Breisgau-Brasilianer as a top-flight side.
"I issued a warning to my team before we played Freiburg. What [Christian] Streich has achieved with Freiburg is sensational," Heynckes told reporters.
"A lot of things have come together over a period of years for them. It was a job that required hard work, but credit to the lads. We were very smart and very professional."
Bayern have still not dropped a Bundesliga point in 2013 following their win at the Allianz Arena.