Murray was due to turn his attention to competing at the China Open, but it has now been confirmed that he has pulled out of the tournament in Beijing due to a slight ankle issue.
Fifth seed Verdasco defeated the former world number one 6-4 6-4 to reach the semi-finals.
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The Spaniard also knocked Murray out of the US Open at the second-round stage in August. The two wins in a month came after Verdasco had previously suffered eight consecutive defeats to the Scot stretching back nine years.
Verdasco will play Yoshihito Nishioka for a place in the final.
Murray, down to 311 in the world rankings, had enjoyed the best win of his comeback by beating David Goffin on Thursday but fifth seed Verdasco was too solid and occasionally spectacular, cracking 11 aces and 38 winners in his one hour 40-minute win.
The Scot will now focus on an intense period of rehabilitation in a bid to fast-track his route back to full fitness in time for the first Grand Slam of next season in Australia.
Murray announced earlier this month that he will miss the ATP Masters events in Paris and Shanghai as he seeks to return to his best possible shape.
Fellow Brit Cameron Norrie also exited the tournament in Shenzhen at the same stage as Murray, with the Japanese Nishioka prevailing 7-6 6-2 earlier on Friday.
Pierre-Hugues Herbert takes on Alex de Minaur of Australia in the other semi, after the Frenchman took just under three hours to overcome Albert Ramos-Vinolas 6-7(4) 7-6(3) 6-4.
World No.40 De Minaur won in straight sets 6-3 7-6(7) against Damir Dzumhur to book his place in the final four.
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