Universidad progressed courtesy of a 1-0 win in the first leg but there was nothing to cheer in a poor follow-up where both sides had a man sent off.
Osvaldo Gonzalez had the best chance for the Chileans in the first half, reaching a cross by Charles Aranguiz but seeing his chance cleared.
Universidad's Guillermo Marino was sent off in the 36th minute after a butting Crisitan Rivero, but Fenix could not take advantage of that and the numbers were levelled after the break when Gonzalo Papa was dismissed.
Universidad will now play another Uruguayan side, Nacional.
Meanwhile, in Colombia, La Equidad claimed a valuable 2-0 win over Peru's Juan Aurich, in the first leg of their first-round tie.
Defender Hanyer Mosquera opened the scoring in the 20th and Juan Nunez doubled the advantage 10 minutes before the final whistle.