Drag flicker Sohail Abbas and experienced forward Rehan Butt scored on either side of halftime Thursday to hand Malaysia its first defeat at Guangzhou.
Pakistan's last Asian Games gold came in 1990 at Beijing. The win here was Pakistan's first major title since winning the World Cup in 1994.
India clinched the bronze, defeating South Korea 1-0 via Tushar Khandker's field goal in the 39th minute.