The reason for Wednesday night's attack on the truck in which Flores, a 58-year-old former Cruz Azul player who featured at the 1978 World Cup in Argentina, was travelling with his family is as yet unknown.
Two adults were also hurt in the attack and a child suffered a nervous breakdown, according to local media. Witnesses said dozens of shots were fired at the vehicle.
"Ignacio Flores Ocaranza rest in peace. Maestro, Friend and Father," his club said on their Twitter account.
The right-back, who won five league titles with Cruz Azul in the 1970s, was a brother of Luis Flores, a former Pumas UNAM striker who also played for Mexico.
Cuernavaca, in the central state of Morelos, and the Pacific seaside resort of Acapulco have in recent years become battlefields for rival gangs of drug traffickers.
Drugs-related violence has claimed more than 42,000 lives in Mexico since 2006.
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