Son put the Koreans in front in the Group C clash in the second phase of Asia's preliminaries with an 11th minute penalty after Hwang Hee-chan had been fouled in the area.
He added the second in the final minute of the first half with a header for Jurgen Klinsmann's side.
The Tottenham Hotspur forward turned provider three minutes from time when he drifted in a free kick from the right that Jung Seung-hyun headed past Yan to put the seal on the victory.
In the opening set China had beaten Thailand who bounced back from that loss to beat Singapore 3-1.
Mohanad Ali scored six minutes into injury time to earn Iraq a 1-0 win over hosts Vietnam in Group F as Jesus Casas' side moved onto six points.
Vietnam remain in second in the group standings after the Philippines and Indonesia shared a 1-1 draw in Manila.
Qatar, the host of last year's World Cup, followed their 8-1 defeat of Afghanistan by beating India 3-0 in Group A.
Japan have opened with a brace of 5-0 wins, winning in Syria by that score after putting a handful past Myanmar.Â
Also in Group B Jong Il Gwan scored a hat-trick as North Korea picked up their first win of the campaign with a 6-1 thrashing of Myanmar in Yangon having started their quest for a place at the finals last Thursday with a draw against Syria.
Tajikistan also won 6-1 with Amadoni Kamolov hitting a brace in their victory over Pakistan in Group G in Islamabad.
Malaysia top Group D with two wins after winning in Taiwan 1-0.
with AP
