Younus, 38, has not yet fully recovered after being infected by the mosquito-borne virus last month.
He will miss the first Test of the three-match series - a day-night game which begins on 13 October in Dubai.
On his last Test appearance, Younus scored 218 as his side beat England by 10 wickets at The Oval in August.
Younus is Pakistan's highest Test scorer with 9,456 runs from 108 matches, and last missed a Test in May 2011 - also against West Indies, in St Kitts.
Although he has retired from limited-overs internationals, Pakistan are on a roll after whitewashing the Windies 3-0 in both the Twenty20 and one-day international series.
Pakistan batsman Younus Khan will miss his first Test match since 2011 after contracting dengue fever before their series against West Indies.