Ashes-winner Wood also missed the third and final Test, which Pakistan won by 127 runs in Sharjah to take the series 2-0.
His latest ankle-related problem again raises questions about the ability of the 25-year-old Wood to play several matches in a row ahead of England's Test series in South Africa, which starts in December.
Wood's place in white-ball squads to face Pakistan has been taken by Yorkshire fast bowler Liam Plunkett.
England national selector James Whitaker said in an ECB statement.
"Mark Wood's ankle condition is well known and while we have managed his workloads over the summer and during the Test series against Pakistan, it has been decided that the sensible course of action is to seek further advice from a specialist.
"Liam Plunkett will replace Wood in both squads and, having featured in the ODI side last summer, his inclusion provides Eoin Morgan (England limited overs captain) and Trevor Bayliss (coach) with an experienced pace bowling option in the squad."
Pakistan and England play the first of four ODIs in Abu Dhabi on November 11. The one-day series will be followed by three Twenty20 internationals.
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