Striker Nguyen Tien Linh scored in the 18th minute to give Vietnam 1-0 lead.
The hosts bounced back strongly but struggled to create any clear chances on their home ground.
After the break, Vietnam continued to dominate the game. Hong Phuoc missed two chances to double the score but just before the hour mark, Linh made it 2-0.
Both Vietnam and China are preparing for the AFC U23 Championship to be held in Thailand in January next year. Vietnam are also getting ready for the upcoming Southeast Asian Games to be held in Philippines later this year.
Guus Hiddink, the current coach of the Chinese team, worked with Vietnamese head coach Park Hang-seo for the Republic of Korea at the 2002 World Cup.