His predecessor, Jorge Alvarado, had stepped down amid accusations of fraud.
Morales, pledging to generate more wealth for the country's poor from the energy sector, has vowed to revitalise YPFB and put it at the heart of the nationalised industry.
In October, foreign energy companies signed new contracts to continue operating in Bolivia under Morales's nationalisation plan.
They agreed to become service providers to YPFB in exchange for a small share of revenue from natural gas sales.
Morales is a close ally of Hugo Chavez, the Venezuelan president, who recently vowed to take a bigger share in foreign-run oil projects in his oil-rich country.
Bolivia has the second-largest natural gas reserves in South America after Venezuela, but it is the region's poorest country.