Boon previously refereed in the three-match T20I series between Pakistan and the West Indies in April 2018.
Hasan Ali is absent from the squad after complaints of back spasm and will undergo rehab at the National Cricket Academy.
The team will depart for Pakistan on Tuesday with the ODI and T20I squads being captained by Lahiru Thirimanne and Dasun Shanaka respectively.
Mohan de Silva claimed he was satisfied with the security arrangements in place in Pakistan but the final decision rests with the defence ministry.
Javed Miandad has urged Sri Lankan players to honor international commitment and asked the SLC to penalize players who have opted out of the tour
Mohammad Hafeez and Shoaib Malik have not been named among the probables as they have received NOC to play in the CPL until October 12.
Mani assured there was no negative feedback from Sri Lanka Cricket and was confident of Pakistan hosting the series.
Babar, the No.1 batsman in T20Is, has been elevated to the post of vice-captain, days after he was confirmed as skipper for Central Punjab.
Sri Lanka's cricket board claimed it will seek the assistance of its government to "conduct a ‘reassessment’ of the security situation."
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