The Malaysian withdrew from a match for the second time in 10 days at the Super 750 badminton event in Bali.
Yamaguchi will face China's Chen Yu Fei in Saturday's semifinal.
Malaysia eventually lost 1-4 to finish second in the group.
Lee Zii Jia beats Kento Momota in the 2021 Sudirman Cup semi-finals.
I could feel the tensions throughout this tournament.
Their recent duels were tight with few points separating the victor and the challenger, thrilling for spectators in the venue or at home, and utterly engrossing thanks to their immense athleticism and skills.