The club management team confirmed the news on Friday.
He is expected to arrive in Vietnam on December 28 and go into mandatory quarantine.
The value of the contract has not been disclosed.
He will not be treated as a foreign player in next season's top-flight division V. League 1, scheduled to kick off on January 16, since he has a Vietnamese nationality.
HCMC FC have been trying to recruit the 34-year-old midfield star since February, agreeing to pay $1 million, from Inter Miami CF, owned by English star David Beckham, but their offer was initially rejected by the U.S. club.
Nguyen played for Hoang Anh Gia Lai (2009-10) and Becamex Binh Duong (2010-11), and was rated highly despite having some trouble adapting to the football environment in Vietnam.
He then returned to the U.S., and was called up for the national team nine times by coach Jürgen Klinsmann.
HCMC also signed Brazilian striker Wagner da Silva Souza from Guarani FC earlier this month, also on a one-year contract.