Rafael Borre converted a spot kick with seven minutes gone after the Brazilian referee consulted with the VAR and adjudged the same player to have been felled in the penalty area.
Ignacio Fernandez doubled River’s lead with 70 minutes gone when he flicked home a Matias Suarez cut back from the right wing.
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Tuesday’s game was a repeat of last year’s final that was due to take place at the same Monumental stadium but postponed after River fans attacked the Boca team bus as it approached the stadium.
The game was eventually moved to Madrid where two weeks later River beat their city rivals 3-1 to lift the Libertadores, South America's equivalent of the Champions League, for a fourth time.
Tuesday's tie got under way in relative peace and with away fans banned from most games in Argentina due to violence by the barra brava hooligan firms, River were greeted by 70,000 of their own fans.
The home side had the better chances in an exciting match, particularly in the second half, with Boca keeper Esteban Andrada making at least three good saves and Gonzalo Montiel hitting the post with a cross that drifted over Andrada’s head and almost squeaked in.
Nicolas Capaldo missed the best chance of the game for Boca two minutes before half time but he blazed over the bar with just the keeper to beat when it looked easier to score.
The youngster’s misery was completed in injury time when he was shown a red card after another VAR intervention.
The second leg takes place at Boca’s ground on Oct. 22 with the victor meeting the winner of the all-Brazilian tie between Gremio and Flamengo in the final in Santiago, Chile on Nov. 23.
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