The two players, who play for English sides Leicester City and Newcastle United respectively, were instrumental in the Black Stars' march to the semi-finals, where they lost to eventual champions Cameroon.
Both players featured in all six Ghana matches at the competition held in Gabon.
Atsu makes the team for the second successive time, having been named in the XI for the 2015 Afcon.
Winners Cameroon had three men in the set-up including goalkeeper Fabrice Ondoa, defender Michael Ngadeu-Ngadjui and winger Christian Bassogog, who was also adjudged Player of the Tournament.
AS Roman attacker Mohamed Salah and defender Ahmed Hegazy were the two Egyptian representatives.
Goalkeeper: Fabrice Ondoa (Cameroon)
Defenders: Modou Kara Mbodji (Senegal), Ahmed Hegazy (Egypt), Michael Ngadeu-Ngadjui (Cameroon)
Midfielders: Charles Kabore (Burkina Faso), Daniel Amartey (Ghana), Bertrand Traore (Burkina Faso), Christian Atsu (Ghana), Mohamed Salah (Egypt)
Forwards: Christian Bassogog (Cameroon), Junior Kabananga (DR Congo)