In Uruguay, Nacional beat Defensor Sporting 1-0 to win the championship, a fitting send off for playmaker Marcelo Gallardo, who brought the curtain down on his career.
'La U', with striker Gustavo Canales scoring a hat-trick including two penalties, won the two-leg final 4-3 on aggregate.
Catolica had midfielder Tomas Costa sent off in the 35th minute for a second bookable offence and defender Alfonso Parot in the 66th for a dangerous challenge.
Catolica's reserve goalkeeper Fabian Cerda was also dismissed from the bench for dissent and Canales was sent off 11 minutes from time.
Catolica players were furious with the dismissals and tried to attack referee Enrique Osses, who needed a police escort to leave the pitch.
In Montevideo, midfielder Tabare Viudez scored with a free kick in the 20th minute in the Uruguayan final between Clausura champions Nacional and Apertura winners Defensor.
Argentine Gallardo, who played at the 1998 World Cup, spent most of his career at his first club River Plate in Buenos Aires with spells in France at Monaco including a Ligue 1 title in 2000 and Paris St Germain.
"It was a dream to finish this way," said 'Babyface' Gallardo at the end of an 18-year career in which he won South America's Libertadores Cup with River in 1996.
The 35-year-old joined Nacional last year and after injury spoilt the Apertura for him, he became a fans favourite in the Clausura and was given a resounding farewell on Sunday having announced his retirement in the week.
