The Round of 64 clash saw the second-tier side come from behind to beat Kotoko 2-1.
Richard Arthur took the lead for the visitors in the 33rd minute. The forward fed off a miss shot my Ibrahim Imoro to tuck it home for the Kotoko.
The striker could have doubled the lead for the Porcupine Warriors but could only steer his effort wide.
Moments later it was Deportivo who came close to finding the equaliser but Felix Annan was on hand to deny Raymond Owusu’s close header.
The host struck home on the 45th-minute mark as Godfred Abban headed home to beat an onrushing Felix Annan who was caught on a no-mans land to end the half 1-1.
Deportivo took the lead for the first time in the game after scoring twenty minutes into the second half.
The lower division side held on as they eliminated the MTN Fa cup defending champions, progressing to the Round of 16 stage of the competition.
The results meant Kotoko have won just once and lost twice in their last six games, a run of form Coach Maxwell Konadu will have arrest sooner rather than later.