It allowed England's Nick Tandy, Bamber's team mate in the 2015 Le Mans win, to pass him and put the other Porsche in front once again, as they would lead for large portions of the race.
However, Bamber's team persevered as they were able to regain the lead at the final pit stop by both crews, and hold it to the finish.
The pole-sitting Toyota TS050 Hybrid crew of Kamui Kobayashi, José Maria Lopez and Mike Conway took third place, while their Toyota Gazoo Racing team mates Anthony Davidson, Kazuki Nakajima and Sébastien Buemi were fourth after an enforced change of fuel pump on the first lap.
The victory moved Bamber's team to 108 season points, 30 points clear of second placed Toyota Gazoo at the top of the driver's championship after the last European round.
The series now heads to Mexico on September 3.