Venezuela has helped Penn's J/P Haitian Relief Organisation distribute medicines in Haiti following the disastrous earthquake in 2010.
According to The AP, Penn praised Venezuela for its financial contributions to the aid effort. He also praised the help that the charity has received from the US military.
"We hope that this kind of collaboration can be an example for future approaches to many other issues," said Penn.
Venezuela has had a strained relationship with the US since Chavez reportedly failed to recognise the White House's nominee for envoy in a diplomatic dispute.
Penn first met Chavez in 2009 when the actor flew to Venezuela to discuss the possibility of shooting a film in the South American country.