Penn objected to the characterization, saying Chavez is a democratically elected leader.
Chronicle Editor Phil Bronstein took the criticism in stride, calling Penn, "a great actor and a great director."
"People get riled up about a lot of things, particularly in this day and age; they get to express themselves. We were more than happy to print his letter," Bronstein said.
A call to Penn's publicist was not immediately returned.
Penn's past writings for the paper included a five-part series in 2005 about his experiences in Iran.
The 47-year-old actor won an Oscar for his role in 2003's "Mystic River." His screen credits also include "I Am Sam," "Sweet and Lowdown" and "Dead Man Walking."
