But with only two-and-a-half Bundesliga seasons under his belt and having never managed a club in European competition, he lacks managerial experience - one reason why young Hoffenheim manager Julian Nagelsmann was discounted by Bayern, for the time being.
Here are three winners and three losers. Heynckes was brought back in mid this season to replace the sacked Carlo Ancelotti.
Earlier in the game, Vidal could have been sent off for a reckless challenge that went unpunished, while Bayern were awarded a penalty after some theatrics from Arjen Robben that many referees would not have given.
Kovac is described as a team player, addressing the need to get along with the club's leaders.
"We can be proud of what we've done here, and all throughout this Champions League".
"As it stands, I will be in charge of Eintracht Frankfurt next year - 100%".
And as Wagner showed for Hoffenheim last season, he can be the target man, winning 88 aerial duels.
Correa also headed against the crossbar, with Bayern looking rattled while star striker Robert Lewandowski struggled to fire.
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.
And Rodriguez is looking forward to lining up against Real in the Champions League last four.
Madrid beat a Bayern team coached by Pep Guardiola home and away in the 2014 semifinals, and also won their 2000 semifinal matchup.
Bobic confirmed that Kovac has an exit clause in his Frankfurt contract.
They wrapped up a sixth straight Bundesliga title last Saturday and are into the semi-finals of the German Cup.
On the threat posed by Ronaldo, the Bayern boss added: "Along with Lionel Messi, he's the best player in the world and I've already talked about him with Toni Kroos".
Set to return to Real when the 2018/19 campaign is over, James had expressed his desire to stay in Germany past his loan deal. According to several media reports, the German is destined for Paris St Germain for the next season.
"The procedure, I think, is extremely questionable, as I said before".
The 31-year-old had played down links of taking over at Bayern, but refused to completely rule out leaving Hoffenheim. The Bianconeri thought they had done enough to at least force extra time.
"You can't always play brilliantly and put the opponent to the wall, sometimes you have to just keep them scoreless", Heynckes said.
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