Midfielder Raul Cascini blasted in the decisive penalty after Andrea Pirlo, Clarence Seedorf and Alessandro Costacurta had missed for Milan in front of a boisterous section of blue and yellow-clad Boca fans among a crowd of 66,000.
"It was a game between the champions of South America and Europe, so logically it turned out to be a battle," said Boca coach Carlos Bianchi who became the first coach to win the annual match three times.
"Towards the end of extra time I felt the Milan players were hanging on for penalties," he added. "I'm very proud of the way we kept attacking. We were even more aggressive with our penalties."
It was a disappointing end for Milan, who had dominated for long periods in their bid to become the first team to win the World Club Cup four times.
Milan coach Carlo Ancelotti paid tribute to his players after a valiant attempt to even the record between Europe and South America, who now lead the series 22-20.
"You have to give credit to Boca. Their defenders closed us down very quickly and the goalkeeper made some terrific saves," he said.
"We are usually so reliable at penalties but today, for some reason, we just couldn't complete the job."
Striker Jon Dahl Tomasson put Milan ahead in the 24th minute, calmly sliding the ball under goalkeeper Roberto Abbondanzieri from eight
LOOSE BALL
But Boca were back on level terms five minutes later when man of the match Matias Donnet hooked in the loose ball after Milan goalkeeper Dida had blocked a flicked attempt from the dangerous Iarley.
Almost straight from the restart, Brazilian Kaka hit the post with a curling right-foot shot from the edge of the box as Milan quickly sought to reassert themselves.
Milan captain Paolo Maldini nearly capped a record fifth appearance in this fixture with a goal in the 61st minute when he latched on to an Andriy Shevchenko knock-down, only for Abbondanzieri to produce a brilliant point-blank save.
However, Boca substitute Carlos Tevez almost snatched a dramatic injury-time winner when his left-foot shot dipped just over the bar after a neat layoff from Iarley.
Milan, who beat Juventus 4-2 in a penalty shoot-out to win last season's Champions League final, converted just one spot kick this time, handing Boca their third World Club Cup title.
The Argentine champions won in 1977 when they beat German club Borussia Moenchengladbach and lifted the trophy in 2000 also under Bianchi.
Boca, who were beaten by Bayern Munich in 2001, won their third Libertadores Cup in four years with a 5-1 aggregate victory over Santos of Brazil 5-1 in July.
Milan previously won the World Club Cup in 1969, 1989 and 1990 and lost in 1963, 1993 and 1994.