Son's go-ahead goal came in the 58th minute when he curled in a right-footed shot from the left-hand side of the box, two minutes after Ji Dong-Won had equalised for the home side. Swansea midfielder Ki Sung-Yueng had opened the scoring in the 11th minute.
It maintained the unbeaten record of South Korea, who now have two wins and a draw from their opening three matches in the final qualification round.
Son took his sparkling form with Spurs in the Premier League onto the international stage after missing the Koreans' previous qualifier against Syria last month.
In Saitama, the Japanese had to rely on a 95th-minute winner from Hotaru Yamaguchi as they prevailed 2-1 against Iraq in Group B.
The victory took them to second behind Australia, whom they face on Oct. 11 in Melbourne, and Saudi Arabia.
With Borussia Dortmund forward Shinji Kagawa left on the bench, Japan appeared to be heading for a regulation victory when Genki Haraguchi flicked home in the 25th minute to give them a 1-0 half-time lead.
But the unfancied Iraqis turned the match on its head in the 60th minute after Saad Abdul Amir's headed goal from a free kick.
And the 2007 Asian champions looked set to hold on, and even pushed for a second goal after a series of corners.
But, with six minutes of stoppage time added, Japan broke Iraqi hearts after a free kick was awarded near the left corner flag.
Hiroshi Kiyotake curled in his set piece, which was volleyed home by substitute Yamaguchi at the top of the box.
It was an important first home victory of this phase of the campaign for the Samurai Blue, who slipped up against United Arab Emirates on Sept. 1.
The chances of China qualifying for their first World Cup since 2002 took a massive hit after they suffered a shock 1-0 loss to Asian minnows Syria in Xi'an.
The only goal of the game came in the 54th minute through midfielder Mahmoud Al Mawas, who capitalised on a defensive mix up, after smart lead-up work from captain Abdelrazaq Al Hussain.
The result leaves the Chinese on a dismal one point from three Group A matches, two of them at home.
Asian champions Australia lost their 100 percent record when former AFC Player of the Year Nassir Al Shamrani came off the bench to score a 79th minute equaliser for Saudi Arabia in Jeddah.
But the draw was enough to keep the Socceroos top of Group B on goal difference from the Saudis.
Al Shamrani's close-range goal came after Tomi Juric had put Australia ahead eight minutes earlier at the King Abdullah Sports City.
Earlier, Taisir Al Jassem gave Saudi Arabia the lead after five minutes before Aussie centre-back Trent Sainsbury equalised for Ange Postecoglou's side just before halftime from an Aaron Mooy corner.
Valencia goalkeeper Mathew Ryan preserved a point for Australia with a sharp save in the 81st minute, but Australia also had late chances to snatch victory.
Also in Group B, a brace from Ali Mabkhout gave United Arab Emirates a 3-1 victory over Thailand.
Mabkhout scored in both halves against a spirited Thailand side who grabbed their first goal of the final round through Tana Chanabut in the 65th minute.
But the Emiratis made sure of the points with Ahmed Khalil's effort in added time.
In Tashkent, Iran secured a 1-0 victory over Uzbkekistan, thanks to a headed goal from Jalal Hosseini that brought an end to the home side's 100 percent record.
The Uzbeks had suffered the setback of losing playmaker Serve Djeparov to injury just before the break.
The only goal of the game came after 27 minutes from Masoud Shojaei's free kick from the righthand side that was headed home by central defender Hosseini to put the Iranians top of Group A.
