After opening their bid for continental glory with a humbling 3-0 defeat to Guangzhou Evergrande, the J.League giants got off to a dream start in the 8th minute when Yosuke Kashiwagi met Marcio Richards' corner with a looping volley that nestled crept just inside the far post.
Muangthong were then dealt a real blow a minute before the half-hour mark when Piyaphon Buntao was handed his marching orders after picking up a second booking for hauling down Tomoaki Makino, but it took the hosts until the 64th minute to double their tally; Kunimitsu Sekiguchi cutting in from the left and curling in a cross that crept all the way into the bottom corner past a confounded Weera Koedpudsa.
Five minutes later, the contest was all but over after Genki Haraguchi emphatically headed home Hirakawa Tadaaki's right-wing cross, before the Twin Qilins' miserable outing in Japan was capped off by an own-goal from Thritthi Nonsrichai in the 78th minute; the defender prodding the ball into his own net while attempting to make an interception.
The Thai side did manage to give the visiting fans at the Saitama Stadium 2002 something to cheer about in injury-time as Dagno Siaka grabbed a consolation, meeting Weerawut Kayem's pinpoint cross with a firm header into the bottom corner.
Elsewhere in the group, leaders Guangzhou Evergrande and third-placed Jeonbuk Hyundai Motors remain unbeaten after both sides played out a 1-1 draw at the Jeonju World Cup Stadium.
Kim Jung-woo fired the K-League side ahead in the 27th minute with a clinical effort from the edge of the area, but the Chinese visitors earned a share of the spoils three minutes after the hour mark when Muriqui latched onto a neat pass by Gao Lin to fire past Choi Eun-sung.
There were no goals in Group E as Buriram United held FC Seoul to a 0-0 draw at the New I-Mobile Stadium, while Japan's Vegalta Sendai failed to find a way past Jiangsu Sainty of China in a goalless stalemate at the Nanjing Olympic Sports Center.
A last-minute goal by Soares Geilson moments after coming on as a substitute ensured Tractorsazi Tabriz remained at the top of Group A with a 3-3 draw at El Jaish.
The Iranian side went ahead through Lopes Flavio Paixao midway through the first half only for Wagner Ribeiro to equalise with the first of his two goals 10 minutes before the break.
Mehdi Seyed-Salehi restored the visitors' lead six minutes after half-time only for El Jaish to again draw level through Martins Adriano's penalty after 67 minutes.
The Qatari side then appeared to have won the game when Ribeiro scored with three minutes remaining only for Geilson to make his dramatic intervention.
The Iran Pro League side lead the group from Al Shabab after they could only manage a 1-1 draw with 10-man Al Jazira.
Hassan Muath Fallatah put Al Shabab ahead on the stroke of half-time only for Khamis Esmaeel to level after 55 minutes.
Matias Delgado was sent off for Al-Jazira with six minutes remaining but the Saudi Arabian side could not take advantage.
A goal five minutes from time by Jamshid Iskanderov saw Pakhtakor go two points clear at the top of Group B with a 1-0 victory at Dubai-based Al Shabab Al Arabi.
The game was heading towards a goalless draw before Iskanderov struck to give Pakhtakor two wins from two games.
Al-Shabab remain bottom without a point.
Lekhwiya are second after a 0-0 draw at Al Ettifaq who claimed their first point of the campaign.
Tuesday's AFC Champions League Results
El Jaish 3-3 Tractorsazi Tabriz
Al Jazira 1-1 Al Shabab
Al Shabab Al Arabi 0-1 Pakhtakor
Al Ettifaq 0-0 Lekhwiya
Buriram United 0-0 FC Seoul
Jiangsu Sainty 0-0 Vegalta Sendai
Jeonbuk Hyundai Motors 1-1 Guangzhou Evergrande
Urawa Red Diamonds 4-1 Muangthong United