Bangladesh are due to play three matches against Kenya in Nairobi on August12, 13 and 15.
They were dropped following their poor performances against Zimbabwe, who beat Bangladesh 3-2 in a One-day series last month.
Omar scored 28 runs in three games and Kapali 33 in two.
''Javed and Kapali have been asked to return home as they were no longer needed for the team at this stage,'' said Mahmudur Rahman, chief executive officer of the Bangladesh Cricket Board.
Captain Habibul Bashar will also miss the Kenya series after fracturing his thumb in during the Zimbabwe series.
Batsman Tushar Imran has been called up to replace him.
Squad: Khaled Mashud, Tushar Imran, Mohammad Rafique, Rajin Saleh, Mohammad Ashraful, Mashrafe Mortaza, Aftab Ahmed, Mushfiqur Rahim, Shahriar Nafees, Shahadat Hossain, Syed Rasel, Saqibul Hasan and Farhad Reza.