The 27-year-old did not play in round five of the Premier League in Exeter on Thursday in the hope of being fit to play in the three-day tournament.
Van Gerwen, the PDC world champion and world number one, was hoping to win a third successive UK title in Minehead.
His withdrawal means that one player who reaches the third round will receive a bye to round four.
As a result of Van Gerwen's injury, Dave Chisnall played two Premier League fixtures in Exeter, while the Dutchman will now play twice in Manchester on 23 March.
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Michael van Gerwen will miss the UK Open, which starts on Friday, after failing to recover from a back injury.