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Michael Ruddy netted a 37th-minute penalty after Mallards keeper Richard Brush had fouled Guillaume Keke.
It was Frenchman Keke who scored the second with a neat near-post flick on 64 minutes.
Ballinamallard could have gone above Ards with victory but it was Colin Nixon's men who came out on top and have now gone three unbeaten.
Before that, the County Down men had lost five Premiership matches in a row.
Ards are level on points with eighth-placed Glentoran who are away to Coleraine on Saturday.
Ards manager Colin Nixon: "I thought it was a well-deserved win.
"We got about them a bit and had a few chances and scored a well-taken penalty.
"In the second half I think we were well worth the win.
"Ballinamallard had reeled us in when we lost a few games in a row, but we are four points ahead of them now and on a good wee run now and."
Ards continued their mini-revival by beating Ballinamallard in Friday's Irish Premiership game in Bangor.