Hoeness had accused Watzke of insinuating that his side is a small club with a small budget while he ridiculed Dortmund's fortunes in Europe in recent years.
Hoeness had claimed he would only congratulate Dortmund if they managed to be successful in Europe as well as at home.
Watzke responded by saying he had nothing to hide and that his club's financial results were there for all to see, hinting that Hoeness could not take losing.
But Hoeness has now called Watzke to set the record straight and congratulate his side on their second consecutive title triumph, secured with Saturday's 2-0 win over Borussia Monchengladbach.
"It's true, Mr Hoeness called me yesterday [Monday] morning and personally congratulated me on the title," said Watzke to the Bild newspaper.
"I found that a very noble gesture."
Bayern's chairman Karl-Heinz Rummenigge has also delivered his praise to the Westphalians with a note on his club's website.
"Dortmund played a very good season and their team showed class and consistency, and therefore they deserve to be 2012 Bundesliga champions," he said.
"Congratulations to their team, their coach and all of the bosses at Borussia Dortmund."
The two teams will battle it out once again this season for the DFB-Pokal on May 12 with Dortmund looking to make it five wins in a row against the Bavarians.