WAFA captain Abukari Ibrahim fouled Elvis Kyei Baffour inside the box and referee Maxwell Owusu awarded the spot-kick
On the hour mark, Baffour converted expertly from 18 yards by sending goalkeeper Ferdinand Sabi Acquah the wrong way for the opener.
Minutes later, the hosts were awarded a free-kick just outside the box, but teenager Daniel Owusu wasted it.
WAFA made a 40th minute substitution by bringing on Lawrence Agyekum, 17, for defensive midfielder Michael Danso.
After a quarter of an hour played, it was WAFA SC who created the first move, but they failed to finish off a nice combination.
In the second period, WAFA effected another change with Sampson Agyapong taken the place of Forson Amankwah.
The latter finished off a curled ball inside the box, but the celebrations did not last for long as Alhassan Mubarak scored on a rebound.
Michael Ampadu thunderbolt had come off the side post and the WAFA players were caught ball watching.
Liberty Professionals are now unbeaten on the road with two away wins and one draw and their first ever win in Sogakope.
For WAFA SC, it is their first defeat at home since 21 January, 2015 when they lost 1-0 to AshantiGold. Read Full Story