Shane Dolan scored on his Ballymena debut as the Sky Blues secured their first win in eight league matches.
Glenn Ferguson men scored in the first minute as defender Chris Rodgers headed in from Ally Teggart's corner.
Dolan, who joined Ballymena from Donegal Celtic, drilled a low shot past Ballinamallard keeper Alvin Rouse five minutes before half-time.
David Cushley wrapped up the victory with a deflected shot from outside the box three minutes into the second half.
Ballinamallard came into the game more in the second half and had some chances but they never really threatened a meaningful comeback.
Ballymena stay in eighth place but will be relieved to have taken three points for the first time since their 10 November win over Crusaders.
Sixth-placed Ballinamallard have now lost five of their last seven fixtures in the Premiership.