Hoeness will soon enter a Landsberg-am-Lech jail for a three-and-a-half-year term for tax evasion after being found guilty during a trial last month.
He stepped down from his role as Bayern's president but Watzke says he will be back before too long.
"The last chapter has not been written in Borussia Dortmund's relationship with Bayern Munich, not this season either," Watzke told Germany's Tz newspaper.
"And the issue of Uli Hoeness in football is far from over either.
"I've actually called him recently to congratulate him from the bottom of my heart for their title, because this title was also very much his achievement."
Watzke also wanted to set the record straight about a "myth" Hoeness had spread in a recent war of words between the two clubs.
Hoeness claimed he had saved Dortmund from extinction by making a personal two million euro loan to the Westphalian club.
"He did indeed lend my predecessors two million euros - but not without an eight percent rate of interest, so it's not like he was being Mother Theresa," Watzke added.
"Those two million euros didn't help at all because we were already bankrupt, close to insolvency.
"My first task was to pay back those two million euros, which we no longer had, and we did that immediately."