Forward Washington scored a 25-yard free kick, Boca defender Hugo Ibarra scored an own goal, and Dodo put the game away with a goal in stoppage time.
The victory snapped a 45-year streak during which Boca had won 12 series against Brazilian teams.
On Tuesday, LDU played to a 0-0 tie with Mexico's Club America that was enough to send it through to the final for the first time. The first leg ended in a 1-1 tie, so LDU won the series on the away goal.
America finished with nine players after Carlos Alberto Sanchez and Alejandro Arguello were sent off.