Rafinha's second-half equaliser for the visitors cancelled out Shingo Hyodo's opener as Gamba moved a point clear of Kashiwa Reysol at the top of the table.
Gamba threatened early through Lee Keun-ho with the forward seeing a goal chalked off in the 12th minute for offside before hitting the post seven minutes later.
Marinos then went in front after 20 minutes when Hyodo blasted home Ariajasuru Hasegawa's pass from just outside the box.
The hosts went close to a second goal through Kazuma Watanabe's attempt in the 34th minute before Yuji Ono headed Yuzo Kobayashi's cross wide shortly afterwards.
After the break, however, Gamba battled back as substitutes Kim Seung-yong and young Brazilian forward Afonso helped their team-mates regain their momentum.
Akira Nishino's side levelled the contest in the 58th minute when Rafinha headed home a cross from Hiroki Fujiharu.
Gamba pressed for a winner and Afonso hit the post from Kim's cross in the 62nd before Marinos goalkeeper Hiroki Iikura denied both Lee and Yasuhito Endo.
"You cannot expect too much away at Yokohama, but we got one point," said Gamba manager Nishino.
"We created chances and put our opponents under pressure but we couldn't break them enough to find a second goal. That is disappointing but I think we showed our style."
Marinos boss Kazushi Kimura said: "We want to beat anyone ranked higher than us but this is all we could do now against them. They are strong, their two forwards in particular."
Elsewhere, Kashima Antlers were held to a 1-1 draw by Nagoya Grampus.
Osvaldo Oliveira's side outplayed the visitors and went ahead in the 77th minute when Chikashi Masuda fired home.
Nagoya were without suspended boss Dragan Stojkovic following his sending-off in a previous game, and were under pressure for much of the game. But in the 82nd minute Josh Kennedy's header came back off the bar before Marcus Tulio Tanaka eventually finished from close range to grab a point.
Omiya Ardija and Cerezo Osaka played out a goalless draw.