Frederic Mendy scored twice as the Singapore Cup holders came from a goal down to beat the Burmese side
Mladen Ristic struck eight minutes before half-time to give the visitors a surprise lead in the Group G encounter at Bishan Stadium but the Protectors put the Yangon goal under intense pressure after the interval and netted three times in 11 minutes.
Qiu Li equalised with a rasping drive before Mendy bagged his brace to give the S.League club their second win in the competition.
Home moved up to seven points with the victory, one behind group leaders Chonburi of Thailand, who drew 3-3 with Hong Kong side Citizen on Wednesday. Citizen are third with four points while Yangon remained at the bottom on two.
The hosts made much of the early running with Yangon goalkeeper Naing Zayar Tun tipping over a shot by Jeremy Chiang after seven minutes before Mendy headed wide from close range.
However, with the majority of the 3,146 fans cheering on the visitors, Yangon gradually got a foothold in the match and provided a constant threat with their pace on the counter-attack.
Yan Aung Kyaw saw a shot from the edge of the Home box deflected narrowly wide and then cut the ball back for Kyi Lin who just failed to find the target with his close-range effort.
Home failed to heed the warning signs and fell behind in the 37th minute after a defensive error by Kenji Arai. The Japanese defender fluffed at his attempt to clear Kyaw's dangerous cut-back from the left by-line and Ristic pounced to send the ball past goalkeeper Lionel Lewis with the aid of a deflection off Arai.
While Home were unable to muster a response before half-time, they came out strongly in the second half and laid siege on the Yangon goal .
Shotaro Ihata's shot from a narrow angle was tipped wide by Tun, Qiu struck the right post with a free-kick and Indra Sahdan Daud fired over the crossbar as the Singaporean side turned up the heat.
Their efforts were finally rewarded in the 69th minute when a corner found Shi Jiayi on the edge of the box and the Home skipper teed up the ball for Qiu, who fired a rising shot from 20 metres into the top right corner .
The hosts took the lead six minutes later as Firdaus Idros sent in an inviting cross from the left which Mendy chested down in the six-yard box before lashing it home with his left foot
The Frenchman sealed the victory with his second of the game in the 80th minute. Qiu was the architect, sending in a low cross from the left flank which Mendy slammed home.
Yangon United coach Eric Williams was disappointed at his team's failure to maintain their poise as they remained winless in the AFC Cup.
"The players are still learning to play at this level but we have made a number of mistakes during this competition that have prevented us from going further," said the Australian.
"We conceded a late goal against Chonburi that led to a draw and a late goal against Citizen that resulted in a defeat. Today, we collapsed in the second half and that was partly because some of our players were playing to the capacity crowd here rather than playing to instructions.
"The players have to learn to follow instructions rather than trying to impress the crowd and doing their own thing."
Home United coach Lee Lim-saeng felt that the victory was merited and gave his side a good chance to top their group.
"I'm very grateful to the players for their work tonight because they never gave up," said the Korean. "I still think Chonburi can be caught and we will be going all out in our next two games to catch them and finish in first place.
"I don't know if we can succeed but why not try?"