He is still recovering from a shoulder injury and has not been declared fit by the ACB medical team to participate in the remaining matches.
Naveen will visit England for his intensive treatment and rehabilitation until he is fully fit.
Fast bowler Abdullah Ahmadzai, who was previously in the reserves and recently made his international debut, has been promoted to the main squad for the Asia Cup.
Afghanistan began their three-match ODI series against Bangladesh with a confident five-wicket victory in Abu Dhabi on Wednesday, chasing down 222 with 17 balls to spare.
Following Bangladesh’s T20 series against Afghanistan, right-handed batsman Saif Hassan has made a significant leap in the ICC T20 rankings. His unbeaten half-century in the final match of the series propelled him 17 places up the list, taking him to 18th position.