First-half goals from Sergio Escudero and Kim Jin-kyu gave the South Korean champions control although they had to hold on when goalkeeper Yu Sang-hun saw red after upending Wilson in the area with three minutes left.
The Brazilian tucked home the spot-kick but Vegalta failed to find an equaliser.
Debutants Jiangsu Sainty claimed their first ever win in Asia's top competition as they overcame Buriram United 2-0.
Lu Bofei and Sun Ke struck within a minute at the end of the first half to move the Chinese side off the bottom of Group E and up to second place.
Japanese champions Sanfrecce Hiroshima's nightmare campaign continued as they were beaten 1-0 by Pohang Steelers.
Bae Chun-suk grabbed the only goal on 18 minutes to leave Sanfrecce without a point at the halfway stage in Group G.
Pohang's win drew them level with Bunyodkor and Beijing Guoan on five points after they played out a goalless draw in Tashkent.
Al Ahli maintained their perfect start with a 4-2 win away to Sepahan at the Foolad Shahr Stadium.
Last year's beaten finalists took control of Group C as Victor Simoes's double inspired them to a third win in as many games.
The Saudis battled back from going behind to Zhevahir Sukaj's third-minute strike with goals from Simoes and Bruno Cesar ensuring they were ahead by half-time.
The game was all but decided when Amad Al Hosni netted a third 50 seconds after the resumption before Simoes rounded the goalkeeper on 65 minutes to complete his brace.
Farshid Talebi grabbed an 87th-minute consolation for the home side.
Al Gharafa remained three points adrift of Al Ahli as they also won 4-2 away to pointless Al Nasr.
The Qataris had to survive a comeback though after Djibril Cisse, Hamed Shami and a Nene penalty had sent them into a 3-0 half-time lead.
Al Nasr hit back around the hour mark with two goals in three minutes from Habib Al Fardan and Bruno Correa but that was the extent of their revival. Lawrence Quaye sealed the win with six minutes left.
Nassir Al Shamrani scored the only goal of the game as Al Shabab won their top-of-the-group battle with Tractorsazi Tabriz.
El Jaish joined Tractorsazi on four points in Group A with a 3-1 win over Al Jazira at the Al Rayyan Stadium.
Wagner Ribeiro scored twice with his opener coming after seven minutes.
Mahir Yusuf doubled the lead soon after and while Subair Khater pulled a goal back in first-half stoppage time, when his free-kick somehow eluded a pack of players to creep in at the far post, Wagner Ribeiro settled the contest on 58 minutes.
Tuesday's AFC Champions League Results
El Jaish 3-1 Al Jazira
Al Shabab 1-0 Tractorsazi Tabriz
Al Nasr 2-4 Al Gharafa
Sepahan 2-4 Al Ahli
FC Seoul 2-1 Vegalta Sendai
Sanfrecce Hiroshima 0-1 Pohang Steelers
Bunyodkor 0-0 Beijing Guoan