A win which puts Fradi in third place, two points behind leaders Fehérvár who however have a game in hand.
Schembri scored on 18, 27 and 76 minutes. Malta goalkeeper Justin Haber was back in the starting line-up and was prominent in saving a penalty.
Meanwhile in England, Daniel Bogdanovic was included as a substitute for Sheffield United but still managed to score and give the Blades a 3-2 win. However in added time, he was sent off.
Sheffield United are now eighteenth with 22 points from 18 matches.