Interim President Manuel Serifo Nhamadjo announced the nomination of 28 government ministers late on Tuesday.
The cabinet, under Prime Minister Rui Duarte Barros, includes Col. Celestino Carvalho - who took part in the coup - as defense minister.
Army Col. Musa Diata, who did not participate in the uprising, was named as junior minister.
The development follows a deal between the country's transitional Military Command and the regional Economic Community of West African States (ECOWAS).
The agreement puts Nhamadjo in place as transitional president, with a 600-strong ECOWAS force to be installed and new elections promised within 12 months.
Members of the armed forces - including members of the Military Command - were set to return to their barracks, the AFP news agency cited junta spokesman Lt. Col. Daba Da Walna as saying.
"Now that the transition government has been formed, the Military Command and the army will return to their barracks," Da Walna told AFP early on Wednesday.
The junta had announced in a press conference on Tuesday, ahead of the cabinet's appointment, that it was handing power back to civilian leaders in the capital, Bissau.
The military took control in an overnight coup on April 12, temporarily detaining interim President Raimundo Pereira and former Prime Minister Carlos Gomes Junior. The putsch came ahead of a presidential election in which Gomes Junior was seen as the likely winner.
'Secret deal' alleged
Coup leaders said Gomes Junior had made a "secret pact" with Angola at the expense of Guinea-Bissau's own military.
Gomes Junior has voiced support for incentives to combat cocaine smuggling and efforts to stop the military from becoming involved in politics. Crucially, he is to be exempted from the next elections, despite having won 50 percent of votes in a first-round election in March.
Since the coup, Gomes Junior has accused ECOWAS of legitimizing coup leaders through negotiation.
Guinea-Bissau has suffered several military uprisings since independence from Portugal in 1974. The UN, along with a body of Portuguese-speaking countries led by Angola, has criticized ECOWAS for not taking a hard enough line with the leaders of the latest coup.
rc/av (AFP, Reuters)