The Chile side had defender Diego Reynoso sent off in the early stages of the second half for hacking down Penarol forward Sebastian Cristoforo - but the hosts held on.
Penarol boss Diego Alonso was pleased with his team's showing, as he said: "They have played seven competitive matches before this one and we have only played two friendly games. That showed on the pitch."
Paraguayan side Libertad clinched a 2-1 win over Uruguayan Wanderers in Montevideo.
Federico Rodriguez headed Wanderers into an early lead but Brian Montenegro equalised with a long-range shot four minutes into the second half and home defender Martin Diaz's own goal gave Libertad the edge.
Ecuadorian giants Barcelona twice came from behind to earn a 2-2 draw from their match at Mineros.
The Venezuela side led in the 21st mintue when striker Angel Chourio volleyed home but Barcelona playmaker Michael Arroyo levelled from the penalty spot two minutes before half-time.
Edgar Jimenez restored the home side's lead from the penalty spot in the 64th minute after Arroyo had been adjudged to have handled by Colombian referee Jose Buitrago.
However, Luis Caicedo tapped in from close range with 10 minutes of the contest remaining to bring Barcelona level for the second time.
In Ecuador, home side Independiente could not find a breakthrough in their match against Venezuelan side Deportivo Anzoategui.
The other game also finished goalless, with Guarani and Bolivia's Oriente Petrolero cancelling each other out in Paraguay.