The 46-year-old will start a three-year contract with Bayern from July 1.
Bayern made it clear only German speakers would be considered for the role, meaning Kovac ticked a box many big-name coaches could not.
Kovac's brother Robert, also a former Bayern player, will join him from Frankfurt as his assistant. It's not so simple, I have to admit. "It's hard for me now that it's ending soon".
Both sides traded blows throughout the first half, with Bayern's Joshua Kimmich and Mats Hummels and Sevilla's Sergio Escudero all coming especially close, but neither could open the scoring by the break.
Volland, with only an outside chance of earning a place in Germany's World Cup squad, scored again six minutes later with an easy tap-in and completed his treble with an nearly identical goal two minutes from time for his 14th league goal this season.
The likes of Thomas Tuchel, Julian Nagelsmann, Jurgen Klopp and Mauricio Pochettino were all linked with Bayern, but in the end it's Kovac who has won the race to lead The FCB.
Kovac is relatively inexperienced - Eintracht was his first club job and he was only appointed in March 2016.
Frankfurt's sporting director Fredi Bobic was furious, accusing Bayern of being "not professional and disrespectful". I hope he doesn't have his best day against us.
"We showed fight with our performance today", he said.
"I've read his biography and it's very positive". In the meantime, they are readying themselves for their new manager. "Not of Eintracht Frankfurt". Frankfurt has a German Cup semifinal match against Schalke next week.
Kovac is described as a team player, addressing the need to get along with the club's leaders. Bayern's loss is Hoffenheim's gain, however, as the young coach can continue to build his team to climb the Bundesliga table. Respect is hugely important in such a collective.
Bayern will have revenge in mind this time around, as they seek to build on the domestic dominance which has already been secured in Germany.
Heynckes replaced Carlo Ancelotti in October after the Italian was sacked following a series of poor result.