Ghana now tops Group H with 6 points from two matches after beating Rwanda 1-0 in Kigali.
Saturday's game, which had a late winner from Mubarak Wakaso, saw Asamoah Gyan not making the bench due to injury, while Jonathan Mensah also reportedly was dropped due to a niggling problem in his legs.
Avram Grant made four changes to the side that thrashed Mauritius 7-1 in Accra. Daniel Amartey, Afriyie Acquah, Andre Ayew and Richmond Boakye-Yiadom replaced Jonathan Mensah. Agyeman Badu,Jeff Schlupp and Asamoah Gyan.
Amartey started his first competitive game since January after getting injured in that game against South Africa.
Afriyie Acquah and Mubarak Wakaso resumed their formidable midfield partnership they built in the last AFCON while Richmond Boakye-Yiadom made his first competitive start in two years.
His last start was Ghana's 2-0 win over Lesotho.
The last time Ghana played at the Amahoro Stadium was in 2003 but they succumbed to a 1-0 defeat to the Amavubi’s of Rwanda which eventually qualified the East African side to their first Afcon tourney in 2004 held in Tunisia.
But this time, Ghana managed to get the win, although it was an extremely hard-fought one.
Mubarak Wakaso scored in the final minutes of the 2017 Africa Cup of Nations qualifier after dogged defending from the Rwandans all game. The newly signed Las Palmas (Spain) scored from a cheeky freekick in the 87th minute.
On a deplorable pitch which had been bashed by both teams' bosses pre-game, Ghana and Rwanda laboured to put passes together, and the game quickly degenerated into a long-ball fest.
The first half ended goalless after the Black Stars kept pressing on but were held back by some impressively defensive tactics from their hosts.
After the interval, the star-studded West Africans were the more determined side, but not even the sight of the EPL new boys Andre, Jordan Ayew, Christian Atsu, Jeffery Schlupp and Baba Rahman, intimidated the Amavubi.
Ghana are now top of the table with six points while Rwanda remain on three points. Both nations will be watching Sunday's other group game between and Mauritius and Mozambique.
Black Stars starting XI:
Razak Braimah, Harrison Afful, Baba Rahman, Amartey, John Boye, Afriyie Acquah, Christian Atsu, Mubarak Wakaso, Richmond Boakye-Yiadom, Andre Ayew, Jordan Ayew
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