However, the major action took part in the second half with Jordan Ayew scoring the opening goal for Ghana in the 63 minute.
The Stars returned a better side in the second half with Jordan taking up his leading role with much goal as a 50th minute free kick from Wakaso hit Matampi in post for the Congolese and returned into play but with no one to connect for the Stars.
Ghana, seeking a first Cup of Nations title since 1982, will play Cameroon next Thursday in Franceville for a final place.
And then there's the outsider, Burkina Faso, which reached the final in 2013 but certainly wasn't expected to be in the semifinals in Gabon.
Morocco had opportunities and Romain Saiss and M'bark Boussoufa both hit the bar while Aziz Bouhaddouz somehow could not connect with Faycal Fajr's driven ball inside the six-yard box in the second half.
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Jordan Ayew gave Ghana the lead in the 63rd minute and Andre Ayew swept in a 78th-minute penalty for the victor after Congo had equalized.
Andre Ayew converted for Ghana in the 74th minute which eventually became the match victor. That hasn't meant much for Ghana, though. "We can't win all the time", admitted their coach Florent Ibenge as the Congolese failed to match their run to the semi-finals two years ago.
The goal set up a thrilling end to a classic encounter settled by Andre Ayew's penalty in the 68th minute following Joyce Lomalisa Mutambala's foul on Christian Atsu inside the box.
Congo's equalizer was a fabulous curving shot from long range by Paul-Jose Mpoku.
Like el-Hadary and Egypt, these Ghanaians have strong ties to African Cup history: The Ayew brothers are the sons of Abedi Pele, a member of the last Ghana team to lift the African Cup more than three decades ago.