The two countries were the only candidates left in the running after the withdrawal from the race of the Democratic Republic of Congo, leaving the 15-man executive committee of African football's governing body to only decide on which country will host in which year.
The decision can be considered a victory for Morocco as both candidates had expressed a desire to host the 2015 edition rather than two years later.
Morocco said the future tournament would help their bid to professionalise football in the north African country while South Africa had sought to sustain momentum gained from a successful hosting of the 2010 World Cup.
Both have previously hosted one Nations Cup - Morocco in 1988 when there were just eight finalists and South Africa in 1996, just four years after the country's return from long-standing sporting isolation.
Morocco and South Africa were engaged in a much fiercer battle for the right to host the 2010 World Cup, which South Africa won in a tight 14-10 vote in Zurich in 2004.
Next year's African Nations Cup finals are being co-hosted by Equatorial Guinea and Gabon.
After that, the tournament will be played every odd year with the 2013 tournament already designated to Libya.
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