The Malaysian duo fought back in the second game and neither pair could open up a significant gap.
He took the first game in 21 minutes at 21-16.
The Japanese pair stunned the world number ones by taking the opening game, before Gideon and Sukamuljo found their stride.
Catch live badminton score and updates from Lakshya Sen vs Viktor Axelsen Final All England Open Match here.
Tournament women's top seed is up against Busanan Ongbamrungphan while Tokyo 2020 gold medallist will be up against Julie Dawall Jakobsen.
It was just a little reminder that anything can happen in Birmingham.