Velez, winners in 1994, must also host the Uruguayan five-time champions at El Fortin in Buenos Aires behind closed doors when they clash again in Group Four next Tuesday.
A club statement said the South American Football Confederation (CONMEBOL) had also fined them $100,000 (£66,000) after fighting between rival fans at the Centenario in Montevideo.
Penarol were fined $14,000 (£9,200), Uruguayan media reported.
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The Argentine champions are "prohibited from selling visitors' tickets to Velez supporters for the remaining group matches, round of 16, quarter and semi-finals should the team reach those stages," said the statement on their website.
Velez will appeal after Thursday's official announcement by CONMEBOL of the sanctions, the club added.
The sanctions are similar in part to those imposed on title holders Corinthians after a young Bolivian supporter was killed by a flare launched by fans of the Brazilian side at their Group Five match at San Jose in Bolivia two weeks ago.
Corinthians were ordered to play all home matches behind closed doors until further notice and their fans banned from away games.
Velez and Penarol will be vying for outright leadership of Group Four. They both have six points from three matches. Emelec of Ecuador have six from four matches after beating Deportes Iquique of Chile 2-1 at home on Tuesday.
CONMEBOL, acting more strictly and quickly this year than has been their custom on incidents in South Americas often violence-marred elite club competition, also ordered a ban of one match on Sao Paulo's Morumbi stadium.
Sao Paulo will play fellow Brazilians Atletico Mineiro at another venue on April 17 in Group Three.
Atletico lead the group with six points after two matches. They are at home to Bolivia's The Strongest on Thursday when Sao Paulo, who have three points, host Argentina's Arsenal.
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