كتب : Omar AbdelAziz
Yasser Al-Qahtani initially put the Saudis ahead in the 14th minute with a powerful header but was cancelled out by Elie Aiboy's strike six minutes later.
Al-Harthi came off the bench to rescue the Arab Nation just two minutes after his introduction.
Deep into stoppage time, Al-Qahtani whipped in a free-kick from the right and Al-Harthi towered to head home the decisive goal.
The victory put Saudi Arabia, who drew 1-1 with South Korea in the competition's opener, temporarily on top of Group D with four points, one ahead of second-placed Indonesia.
Korea lie third on one point before they take on the pointless Bahrain on Sunday.
Elsewhere, Uzbekistan thrashed co-hosts Malaysia 5-0 in the Group C clash at the National Bukit Jalil Stadium.
Dynamo Kyiv ace Maksim Shatskikh opened the scoring after ten minutes, Timur Kapadze doubled Uzbekistan's lead at the half-hour, and Ulugbek Bakayev added a penalty at the stroke of half-time.
Five minutes from time, defender Aziz Ibrahimovic made it four, before skipper Shatskikh completed what he started with an 89th minute striker.
Uzbekistan have three points from two games as they tie China and Iran, but the duo will clash on Sunday, while Malaysia are dumped out after suffering their second straight 5-0 drubbing.