Carlos Castillo Rangel, the surgeon who treated Hernandez, was quoted as saying that the 34-year-old ex-athlete was in "very serious" but stable condition after being hit in the left, frontal area of his head.
Hernandez was at the "Queen of Kings" nightclub in the central state of Mexico on Sunday when three gunmen burst in and shot at customers, killing two people and seriously wounding two others, the prosecutor's office said.
Hernandez, who serves as sports secretary for the ruling Institutional Revolutionary Party (PRI) in Mexico state, underwent three surgeries after being struck by a 9mm bullet.
"The surgeries were successful, without any complications. We must wait and see his progress in intensive care," Castillo Rangel said.
Bars are often raided by gang members in Mexico, a nation beset by a drug war that has left more than 60,000 people dead in the past six years.