The Thai captain opened the scoring at the National Stadium in Singapore in the second minute and added another just after the interval.
Goals by Supachok Sarachat and Bordin Phala then put the five-time champions in firm control ahead of the second leg on Saturday.
Indonesia’s disappointment in the competition looks set to continue. They have been beaten in their previous five appearances in the final including losses to the Thais in 2000, 2002 and 2016.
Thailand made seven changes to their starting line-up after their semi-final victory over defending champions Vietnam, but they started strongly and went in front after less than 90 seconds.
Philip Roller showed great persistence to get past two defenders on the right of the box before squaring for Chanathip to fire home.
The Thais almost extended their lead in the 14th minute when Bordin’s effort was cleared off the line and came back to Yusef Elias Dolah who headed over the crossbar.
Despite Thailand’s dominance, Indonesia had a chance to get back on level terms just before the interval when Alfeandra Dewangga blazed over with only goalkeeper Siwarak Tedsungnoen to beat.
The Thais tightened their grip with their second goal seven minutes after the interval.
Supachok was surrounded by three defenders in the Indonesian box but he laid the ball off for Chanathip to place a low shot past Nadeo Argawinata for his fourth goal of the tournament.
Irfan Jaya missed a golden opportunity to narrow the deficit when his effort was stopped by the feet of Siwarak.
And the Indonesians would rue that miss as Supachok rifled home a shot from outside the box to make it 3-0 in the 67th minute before Bordin completed the rout with his side’s fourth seven minutes from time.