The changes, announced late on Thursday, underline the uncertainty at the top of Afghanistan's security apparatus that has hindered the fight against the Taliban and other insurgents since Ghani's National Unity Government came to power in 2014.
Stanekzai, who was well regarded by NATO commanders but never confirmed in office by parliament, moves to take over the NDS, whose director, Rahmatullah Nabil, resigned in December after disagreeing with Ghani's moves towards rapprochement with Pakistan.
Stanekzai is replaced as caretaker defense minister by General Abdullah Khan, previously chief of staff at the ministry.
Both appointments will have to be approved by parliament, which failed to confirm Stanekzai as defense minister for well over a year amid wrangling in the government led by Ghani and Chief Executive Abdullah Abdullah, the two rivals in a disputed 2014 election.
Last month, parliament approved former army general Taj Mohammad Jahid as interior minister after the previous incumbent, Noor-ul-Haq Olomi, resigned following heavy criticism over deteriorating security.
At the time, the speaker of parliament asked the government to present nominees to lead the defense ministry and the NDS so that the caretaker arrangement could be ended.