The two Ghana Premier League sides settled for a goalless draw after 90 minutes at the El Wak Stadium.
Both sides lacked the cutting edge as hatful of scoring chances were missed in the two halves.
Perhabs Inter Allies paid for the nine changes made to the their starting line up as they lacked solidity.
In the shoot-out, captain Samuel Sarfo scored first but Abdul Halik Hudu missed his kick.
Frederik Ansah then made it 2-0 before Farid Ibrahim found the back of the net.
Gerald Arkeson scored for Liberty and Ismael Ntefuni also converted his kick.
Liberty keeper Fatao Dida threw his away and Samuel Bekoe could not take advantage as he shot feebly into Dida's hands.
Veteran striker Ernest Papa Arko converted the last kick to put the Dansoman-based side through. Read Full Story
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