The governing body said in a statement that CONMEBOL's appeals committee "confirms the Nov. 29 decision dictated by its Disciplinary Tribunal," to reject Boca's claim.
The club made no immediate comment on Thursday.
Boca wanted CONMEBOL to award them the second leg that was postponed twice due to violence. The arch rivals drew the first leg 2-2 at Boca's Bombonera ground on Nov. 11.
River fans threw missiles at the Boca coach as it approached the Monumental stadium for the Nov. 24 match, injuring several players and forcing the match to be called off.
The violence prompted CONMEBOL to shift the decisive match to Madrid where the teams will meet on Sunday at Real Madrid's Santiago Bernabeu stadium to decide the title.
Boca based their appeal on a similar situation three years ago when they themselves were kicked out of the Libertadores after Boca fans attacked River players with pepper spray at halftime during the first leg of their last 16 showdown. (Editing by Ken Ferris)
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