Nepal clinched the three-match ODI series 2-1 after securing a four-wicket win in Dubai on Monday.
Anwar scored 87 while Boota remained unbeaten on 59 (31) as the hosts collected 114 runs from the final 10 overs.
In reply, Nepal lost opener Binod Bhandari early with Mohammed Naved picking up his wicket.
Captain Paras Khadka rose to the occasion, hitting a fine century to help chase down the target. Nepal reached 255-6 in the 45th over.
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