Master marksman Gary Twigg scored his fourth goal in four games to boost Portadown's hopes of securing a top six finish in the Irish Premiership.
Aaron Burns had the best chance of the first half for the Ports but his effort went wide of the post.
Twigg fired a left-foot shot into the bottom corner of the net after the ball fell to him just after the hour mark.
David Miskelly made fine saves from Jason McCartney and Chris Curran to ensure that Portadown took the points.
Ronnie McFall's side move to within one point of sixth-placed Glentoran, while Ballinamallard remain fourth.
"We are not in the position we would like, but hopefully this result will give us the boost we need and we can kick on from here," said Twigg.
"Personally, I am not as sharp as I would like, but I am improving all the time," added the former Shamrock Rovers forward.
Portadown entertain Glentoran in their next league fixture on 2 February, while Ballinamallard face Coleraine at Ballycastle Road.