Messi was one of a number of high-profile figures in attendance for one of the most exciting finals in the history of the competition.
The first leg ended 2-2 took place a day later than scheduled due to heavy rain in Argentina.
However, the second leg was postponed last month after an attack on the Boca bus as it was on its way to the game.
The match was then expected to take place a day later but was postponed again by CONMEBOL given Boca were still not in the right state of mind to play.
Eventually it was decided that the match would take place at the home of Real Madrid, allowing some of the best players and coaches in Europe to attend the match.
Messi, fresh from his brace in Barcelona's 4-0 win over Espanyol on Saturday, could be seen in the stands with his son.
Atletico Madrid manager Diego Simeone, who made over 100 appearances for Argentina as a player, was also in attendance.
Bayern Munich midfielder James Rodriguez, who is currently serving the second year of his two-year loan spell from Real Madrid, returned to Santiago Bernabeu to watch the finale of South America's most prestigious competition.
Argentina forward Paulo Dybala was also pictured at the match, alongside fellow Juventus team-mates Giorgio Chiellini, Leonardo Bonucci and others.
Atletico Madrid and France star Antoine Griezmann snapped himself in some Boca Juniors gear ahead of the match on Sunday evening.
Noche especial 😍 Love Football ❤️💯 pic.twitter.com/tjzLebCYqm— Antoine Griezmann (@AntoGriezmann) December 9, 2018
Griezmann was joined by Atletico team-mate Diego Godin at the home of their great city rivals.