In a statement to the South American football federation CONMEBOL, the Argentinian club said the team would leave for Spain "Wednesday at 1400 local time (1700 GMT) in a charter flight from Ezeiza airport".
Boca then refused to play the match and it was postponed 24 hours, only to then be called off indefinitely the next day.
Boca petitioned CONMEBOL to be awarded the trophy, but that was rejected.
The first leg at Boca Juniors' Bombonera Stadium had finished 2-2.
CONMEBOL then switched the match to Madrid, a decision opposed by both Argentinian clubs.
Boca have not announced the timing of their team departure although, according to the local press, the indications are that they will leave on Tuesday evening with fans preparing farewell festivities for Tuesday afternoon in the neighborhood of La Boca.
In Spain, 20,000 additional tickets for River fans not residing in Argentina sold in a few hours, a source close to the organisation told AFP.
Another 20,000 for Boca fans living outside the country will go on sale from Tuesday.
The second leg of the Libertadores Cup takes place in Madrid on December 9.