Milito Scores Twice As Inter Grabs UEFA Champions League
The Portuguese tactician, in what could well be his last match in charge of the Serie a side, became only the third coach in the history of the tournament to win the trophy with two different sides.
Mourinho's final act as Porto boss was guiding them to European glory in 2004, and Inter fans will fear history repeating itself following his dress rehearsal at Real Madrid's Santiago Bernabeu, the ground he could call home next term.
Bayern enjoyed much of the possession but struggled to create clear-cut chances despite the constant probings of Arjen Robben and were undone by two breathtaking finishes from Milito.
The Argentina international broke the deadlock in the 34th minute when he nodded on Julio Cesar's long clearance to Wesley Sneijder. The Dutchman returned the ball to his team-mate who showed superb composure to beat Hans-Jorg Butt in the Bayern goal.
Louis van Gaal's German double winners pressed again in the second period, but were again hit on the break with Milito bamboozling Daniel van Buyten before calmly firing beyond Butt once again to seal the treble for Inter and their first European Cup in 45 years.
For Bayern coach Van Gaal, who was mentor to a young Mourinho at Barcelona, the defeat ended his chance to conquer Europe with two separate clubs having won the title with Ajax in 1995.
The match was billed as a clash of contrasting styles between the attacking philosophy of Van Gaal and the defensive proclivity of Mourinho, but there was little to separate the two sides early on.
The biggest threats came from two players who were returning to the Bernabeu having last summer been jettisoned by Real Madrid in the wake of the Spanish giants' 250million euro spending spree.
For Bayern, winger Robben was proving a persistent menace down the right, while for Inter, playmaker Sneijder was superb throughout.
And it was the Nerazzurri playmaker who came closest to breaking the stalemate during an evenly-fought opening 30 minutes.
The dead-ball specialist tried his luck from a free-kick 35 yards out, and Bayern goalkeeper Butt needed to dive to his left to parry the ball away after it had taken a slight deflection off his team-mate Hamit Altintop.
Sneijder, who was one of four former Madrid players in an Inter side without a single Italian, was involved in most of his side's attacks and it was no surprise to see him play a key role in the opening goal of the game.
Julio Cesar's long punt forward was headed down by Milito to Sneijder, who immediately set his team-mate through the heart of the Bayern defence.
The 30-year-old Argentinian powered into the area before leaving Butt with no chance to save with a rising shot.
Bayern, who were without suspended French star Franck Ribery, tried to respond quickly but, after long-range efforts from Altintop and Robben had failed to worry Julio Cesar, they almost found themselves trailing 2-0 just before the break.
Once again it was Milito and Sneijder involved, but with the roles reversed this time.
Milito picked out Sneijder running into the box and it needed a good block by Butt to keep out the former Ajax man's left-footed shot.
Bayern, who were out much quicker than Inter following half-time, had created little to test Julio Cesar in the first half but they almost fashioned an equaliser 25 seconds after the restart.
Ivica Olic's clever flick found Altintop in space and the Turkish international then fed the unmarked Thomas Muller on the edge of the Inter area, but the 20-year-old was denied by the feet of Julio Cesar.
Moments after that Inter launched a breakaway that almost resulted in a second goal, Goran Pandev's shot being superbly tipped over one-handed by Butt.
That was a thrilling start to the second period and Bayern were enjoying plenty of possession as they sought an equaliser.
However, the Inter defence, like it was in the semi-final second leg against last season's European champions Barcelona, was proving tough to break down.
Robben almost managed it with a curling 20-yard effort that brought a brilliant save out of Julio Cesar, while Muller saw a goal-bound effort blocked by the head of Esteban Cambiasso.
Bayern were dominating possession but they were hit with the ultimate sucker punch in the 70th minute as Inter broke away to double their lead.
Milito still had plenty of work to do when he picked up Samuel Eto'o's pass 35 yards out but he superbly turned Van Buyten inside out before coolly finishing past Butt.
There was no way back for Bayern after that as Inter held on to end their long wait for European football's top trophy and perhaps give Mourinho a winning send-off.