The Argentinian side will face Brazil's Corinthians in the final after a 2-0 aggregate success following their first-leg win a week ago, which came thanks to goals from Santiago Silva and Juan Sanchez Mino.
Boca had chances to extend their lead further in the first half, starting in the seventh minute when Juan Roman Riquelme volleyed against the crossbar. Pable Mouche then missed two one-on-one opportunities before Universidad finally mustered a goal threat, with Junior Fernandes' header well saved by Agustin Orion.
The Chileans improved in the second half and twice hit the crossbar, through Marcelo Diaz and Raul Ruidiaz, while Osvaldo Gonzalez tested Orion and Matias Rodriguez headed just wide.
Reflecting on Universidad's fourth semi-final exit from the competition, Diaz said: "We gave our best, but we didn't lose the tie here, we failed in Buenos Aires." Coach Jorge Sampaoli added: "We have no regrets. We are very clear that we made history for the club."
Victory over the two legs sees Boca match the record of ten Libertadores final appearances held by Uruguayan side Penarol. And captain Riquelme, who led his side to victory in 2007, said: "We played very well. I think we had to kill off the tie in the first half, when we had a lot of chances. Then we suffered tiredness, but thanks to God we were not at any risk."
Looking ahead to the final, he added: "This is very important for Boca. The club didn't participate in the last two editions, but we returned and showed we are a big team by reaching the final. Corinthians play good football and will be tough opponents. I'm sure it will be a hard final."
Corinthians reached their first ever final with a 1-1 draw against Santos yesterday to complete a 2-1 aggregate win.
The first leg of the final will be played next Wednesday at La Bombonera stadium, Buenos Aires, with the return match seven days later at Pacaembu.