Bayern also announced that 46-year-old Niko Kovac will take over as their coach and confirmed new contracts for their golden agers, Franck Ribery and Arjen Robben.
"But we made a decision to let them know as soon as possible, now they have more time to get a new coach", Hoeness added.
Treble-chasing Bayern face Bayer Leverkusen in the German Cup semi-final on Tuesday - and Real Madrid in the Champions League last four the following week. The 44-year-old Robert Kovac also previously played for the club.
Kicker magazine reported that Bayern would pay a fee of 2.2 million euros ($2.7 million) to trigger a release clause in Kovac's existing contract with Frankfurt.
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Bayern have won four of the six previous last-four ties between the two clubs, starting with a 3-1 aggregate victory when the clubs first met in 1976.
Kovač has guided his Eintracht Frankfurt side to within touching distance of a place in the Champions League next season.
"We deliberately didn't say anything about it yesterday because we found the comments of Fredi Bobic to be quite outrageous", he said. That's why this point in time is not a very fortunate one for us.
But, there is the risk that their final weeks of the season could see a downturn in form as Kovac's mind begins to shift towards Bayern - who Frankfurt could go up against in the DFB-Pokal final should they win their respective semi-finals. "Obviously the timing of this announcement is inconvenient".
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Kovac arrived at Frankfurt in 2016 and has led them from the brink of relegation to a possible European spot for next season with them sat in sixth and five points off Bayern Leverkusen. "The players must know each other and respect each other".
Frankfurt now lie in 6th place in the Bundesliga, five points away from Champions League qualification, with four games to go.
Bayern was initially in talks with former Borussia Dortmund coach Thomas Tuchel, but he informed the club that he had agreed to take over another team while it was still trying to convince Heynckes to stay.
James was introduced at the start of the second half and played his part in Thiago's goal.
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