Second half goals from Robert Sowah Addo and Joseph Esso earned the Phobians all three points in the Zone B fixture at the Accra Sports Stadium.
Kim Grant's outfit, who lost to Wafa in the previous matchday, have now moved to third on the standings, five places above Allies.
Elsewhere in Zone B, Karela United pipped Liberty Professionals 1-0 in Anyinase thanks to Enock Gator Treku's fifth minute strike. The former have claimed the top spot from Wafa while the latter now occupy the fifth position.
Wafa's downward slide has been due to a 1-0 loss to Ebusua Dwarfs, who were bottom of the table coming into the matchday. Albert Gaisie's 23rd-minute penalty was the decisive factor in Cape Coast. The Crabs, with the three new points, have moved up by one place on the table.
Seventh-placed and hosts Dreams FC and fourth-positioned Elmina Sharks, meanwhile, had only settle for a 0-0 draw in Dawu.
In Zone A, leaders Asante Kotoko returned to action with a 2-0 home win over second-from-bottom Berekum Chelsea at Kumasi's Baba Yara Sports Stadium. Emmanuel Gyamfi broke the deadlock for the Porcupines in the 51st minute and top scorer Abdul Fatawu Safiu scored the second to take his goal tally to six.
Medeama dropped two points following a 1-1 draw with third-placed Aduana Stars but they still hold on to the second position on the table. Bright Adjei netted for the former while the latter struck through Kalibo Dedy Toussaint.
In the last game, Eleven Wonders were held to a goalless stalemate at home by Bechem United in Techiman. The result has left the two teams sixth and fifth on the standings, respectively.
The match between Ashanti Gold and Stallions FC (formerly Wa All Stars) has been postponed.