The Argentine six-times South American champions took the semi-final tie 2-0 on aggregate having won the first leg by that score at La Bombonera in Buenos Aires last week.
Corinthians completed a 2-1 aggregate win over fellow Brazilians Santos, the title holders, on Wednesday.
Boca playmaker Juan Roman Riquelme took the early initiative, looking for openings for the strikers and volleying a shot against the bar from Pablo Mouche's cross in the 8th minute.
Boca goalkeeper Agustin Orion had to make a sharp save in the 23rd minute from a header by Junior Fernandes at a free-kick taken by midfielder Marcelo Diaz.
'La U' had more of the ball and did most of the attacking but were less incisive than Boca and they were lucky not to be at least a goal down to the Argentines at the interval.
Riquelme twice put Mouche clean through on goal in the space of two minutes but the striker lost control with the first opportunity and goalkeeper Johnny Herrera covered well to save the second.
The home side had two near misses in the second half, the first when a 54th minute Diaz free kick hit the post.
With 10 minutes remaining, Universidad's Peruvian substitute forward Raul Ruidiaz was also denied by the post.
The two-legged final will be Boca's 10th and Corinthians' first. The Argentine side are at home in the first leg next Wednesday.