Aliou Cisse's side was comfortably the better team in the first half and it went ahead in the 28th minute when Famara Diedhiou coolly slotted past Jesus Owono after being played in by Sadio Mane.
Equatorial Guinea thought it had been given the chance to draw level shortly after the interval when Iban Salvador clipped against Kalidou Koulibaly's hand in the penalty area, but referee Victor Gomes overturned his initial decision after being encouraged to review the incident by the VAR.
Equatorial Guinea was not to be denied in the 57th minute, though, Jannick Buyla controlling Pablo Ganet's pass and firing past Edouard Mendy before the Senegal goalkeeper could set himself.
Kouyate needed just three minutes after being introduced from the bench to restore Senegal's advantage after 68 minutes, flicking home after a mix-up in the opposition defence, while fellow substitute Sarr wrapped up the win with a simple finish 11 minutes from full-time as his side reached the semi-finals in consecutive tournaments for the first time.
Senegal will face Burkina Faso, which beat Tunisia 1-0, in Thursday's (AEDT) last-four clash.