The A-League's all-time leading goalscorer scored twice in last weekend's 3-1 triumph over Melbourne Victory and came back to haunt another of his old teams in Queensland.
Left unmarked, Berisha skilfully turned Aaron Calver's cross past Jamie Young to double United's advantage on the stroke of half-time.
The visitors had gone ahead in the 11th minute when the excellent Alessandro Diamanti picked out Connor Pain's run to the back post.
Brisbane dominated possession but created next to nothing going forward, with Filip Kurto only forced to make one real save from Roy O'Donovan.
Robbie Fowler's side, hammered 5-1 at Sydney FC last time out, could slide to the bottom of the table if Central Coast Mariners gain a result against Sydney FC on Saturday, while Mark Rudan's men momentarily move up to third.