Historical accounts say Bolivar died of tuberculosis in 1830 but Chavez, who announced the exhumation on Twitter Friday, said he suspects murder, CNN reported.
Forensics exams started in Caracas after completion of the 19-hour exhumation, which began Thursday, the Latin American Herald Tribune reported.
"Bolivar is alive. Let us not see him as a dead man and let us not see him as a skeleton. He is like lightning, like a sacred fire," said Chavez, who views Bolivar as a hero.
State television showed the skeletal remains of Bolivar as the national anthem played and scientists rolled up a black cloth to reveal the skeleton before the broadcast went dark.
Chavez said DNA tests will be conducted on the remains and clothing in the tomb.
The president said he cried when he first saw the remains of Bolivar, who he called the "father of the revolution."
As a political leader and general, Bolivar led troops that liberated Bolivia, Colombia, Ecuador, Panama, Peru and Venezuela from the Spanish crown and is widely credited with fostering democracy in Latin America.