The 2008 Asian champions said in a statement on their website they had informed Miyamoto of the decision on Thursday evening.
Two-time J-League champions Gamba, who last won the domestic title in 2014, have recorded just one win in 10 games of the new campaign and are 18th of 20 teams.
Named J-League manager of the year last season after leading the club to second behind Kawasaki Frontale, Miyamoto will be replaced on an interim basis by Masanobu Matsunami.
Gamba are one of four teams from Japan set to play in the AFC Champions League next month. They are due to face Jeonbuk Hyundai Motors from South Korea, Singapore's Tampines Rovers and Australian champions Sydney FC in the group phase.