The Brazilian club's 2-0 win in the second leg of the final followed a 1-1 draw at La Bombonera in Buenos Aires last week.
Emerson struck nine minutes into the second half, pouncing on playmaker Danilo's back-heel after Boca's defense failed to clear the ball from a free-kick.
The 33-year-old then doubled the lead in the 73rd minute, seizing on an errant pass from Boca defender Rolando Schiavi to race forward and coolly slot the ball home.
The win means Corinthians will go to Japan in December for the FIFA World Club Cup.
"The group deserved it, they worked hard, no one did more than Corinthians," manager Tite said after the final whistle. "It wasn't by chance, it wasn't luck, it was fully deserved. The magnitude of it all hasn't sunk in yet."
The triumph was greeted with an outpouring of relief by a crowd of over 40,000 fans. For decades Corinthians fans had suffered as the only one of Sao Paulo's big four sides not to have won the continent's biggest club tournament.
The result means Corinthians went through the competition unbeaten, conceding just four goals in 14 games.
That defensive strength was evident throughout a match which began with a tense and error-strewn first half in which neither club made many clear chances.
The second half was slightly better and started with an early onslaught from the visitors as they won three corners in the first four minutes.
However, it was Corinthians who took the lead after Emerson seized on Danilo's flick to poke the ball home from six yards.
The goal settled the home side and with Paulinho dominating midfield and the defence well-organised they never looked likely to surrender their advantage.
Boca did come close with a header that was well saved by Cassio in the 72nd minute, but that was to be their last hope. Just seconds later Schiavi gave the ball away and Emerson sprinted 45 yards to slide the ball home and end the match as a contest.
Boca had been seeking a seventh title that would have taken them alongside Independiente as the tournament's most successful club.
