Cavalry officers in 19th-century uniforms carried the coffin into the academy's courtyard, where more than 1,000 cadets rendered honours to the one-time paratrooper.
Chavez, 58, died March 5 after a nearly two-year battle with cancer and his state funeral took place last Friday, but authorities decided to keep the glass-covered coffin at the military academy for an extra week to give as many people as possible the chance to pay their final respects.
Leading the procession across the courtyard to the street were the dead president's parents, accompanied by other family members, senior officials and Venezuela's military brass.
Bolivian President Evo Morales, one of the more than 30 world leaders who attended last week's state funeral, was also present as the cadets sang the traditional military anthem "Patria querida" (Beloved Homeland) and canons fired volleys.
Combat aircraft flew over the academy during the ceremony, which followed a Mass and remarks by Chavez mentor Maj. Gen. Jacinto Perez Arcay, National Assembly speaker Diosdado Cabello and one of the late president's daughters, Maria Gabriela Chavez.
First elected in 1998, Hugo Chavez won another six-year term in last October's presidential contest.
He took to the airwaves two months later to tell Venezuelans he was travelling to Cuba for a fourth operation to deal with the cancer that was diagnosed in June 2011.
The man Chavez designated as his successor, Vice President Nicolas Maduro, became acting head of state last week and will represent the governing leftist PSUV party in next month's special election.