Velez, champions in 1994, beat Penarol 2-1 in an exciting second leg of their semi-final at the Fortin but the visitors edged the tie after registering a 1-0 victory in Montevideo.
Penarol, who lifted the last of their titles in 1987, will meet twice champions Santos over two legs in the final after the Brazilians beat Paraguay's Cerro Porteno 4-3 on aggregate on Wednesday.
It will be the second final meeting between the sides in 49 years after Pele's Santos beat Penarol in 1962.
Velez will pinpoint three key moments that cost them a chance of victory, when they first had a goal disallowed for offside, had central defender Fernando Ortiz sent off in the 69th minute and then saw striker Santiago Silva miss a late penalty that would have put the Argentine's through.
Penarol shocked Velez by taking the lead in the 34th minute to move 2-0 ahead on aggregate, just reward for their better play up to that point.
Alejandro Martinuccio linked in the middle with fellow striker Juan Manuel Olivera and fed the ball left, where midfielder Matias Mier shot under goalkeeper Marcelo Barovero.
Velez striker Juan Manuel Martinez had a goal disallowed near the end of the first half for offside - an incorrect decision according to video replays - and tempers flared just before halftime when Silva went down with his marker Carlos Valdez and the home side claimed a penalty.
However, the Argentine side equalised in first-half injury time when goalkeeper Sebastian Sosa failed to hold a Maxi Moralez free-kick and substitute right back Fernando Tobio bundled the ball in.
PENALTY MISS
Olivera missed a good chance to put the match beyond Velez in the 67th minute when Argentine Martinuccio set him up with only Barovero to beat, but he sliced his shot wide.
Within a minute, Silva had fired Velez in front off the post but the joy was short-lived when Ortiz was dismissed minutes later for a foul on Martinuccio, having been shown his first yellow card in the first half for dissent.
Martinez earned 10-man Velez a penalty with quarter of an hour remaining and a chance to go ahead for the first time in the tie when he was brought down on the edge of the box.
However, when Uruguayan Silva took the spot-kick, his supporting foot slipped as he shot and the ball ballooned over the bar.
The Uruguayans' joy at the final whistle, not least their brilliant 45-year-old coach Diego Aguirre, who scored the winning goal for their 1987 title-winning side, contrasted dramatically with the pain on the faces of the Velez fans.
"I'm very happy going back to a final with Penarol with all the history we have," Aguirre said.
"It was obvious we didn't came here to defend, we came to play, as we have done up to now. That's why I think it's right that we should be living this dream," he told Fox Sports.
"I'm proud to be with this group (of players) who are returning to the glory (d
