The two were involved in a war of words earlier in the season as their respective clubs battled it out for the German crown.
However, Dortmund general manager Watzke has revealed that Hoeness phoned to congratulate his team for retaining their title and thanked him for the "noble gesture".
"It's true, Mr Hoeness called me yesterday morning and personally congratulated me on the title," Watzke told German newspaper Bild. "I found that a very noble gesture."
Dortmund could complete a double by beating Bayern in the German Cup final on May 12.