Murray admits he lost focus after being forced to replay a break point disrupted by a loud noise in the fourth set – which he went on to lose 6-1.
Nishikori will take on Stan Wawrin next – after the Swiss beat Juan Martin Del Potro.
Meanwhile, Serena Williams was pushed hard by fifth seed Simona Halep before coming through in three sets to to reach tonight's semi-finals.
The six-time champion, who won 6-2 4-6 6-3, will play 10th seed Karolina Pliskova in the last four.
Second seed Angelique Kerber takes on two-time finalist Caroline Wozniacki in the other semi.
