Rafinha pounced on a back pass from Shin Kanazawa and fired a shot, which was saved by goalkeeper Takashi Kitano, but Lee quickly hit the rebound into the empty Omiya net in the 43rd minute.
A long ball from Japan international midfielder Yasuhito Endo was picked up on the right by Korean midfielder Kim Seung-Yong who hit it into the area to allow Rafinha to score the second goal in the 77th minute.
Gamba Osaka now have 53 points, ahead of Yokohama Marinos and Kashiwa Reysol on 50 points, defending champions Nagoya Grampus on 49 points, and Kashima Antlers on 39 points.
Ariajasuru Hasegawa scored the only goal in Yokohama's victory over bottom placers Avispa Fukuoka, while Kashiwa came back from a goal down to beat Nagoya 2-1.
Seven-time champions Kashima also came back from two goals down thanks to late scores from Daiki Iwamasa and Yuzo Tashiro which earned them a 2-2 draw against Albirex Niigata.
In other games, Cerezo Osaka scored five goals in a second-half onslaught, including a hat-trick from Ryuji Bando, to beat Sanfrecce Hiroshima 5-4, while Jubilo Iwata won a Shizuoka derby against Shimizu S-Pulse 2-1.
