Halifax made a blistering start to the second round tie at St Giles Road, Jason St Juste and Jamie Rainford scoring to put them 2-0 up after 20 minutes.
Shane Hamilton reduced the deficit on the hour before substitute Reece Richards netted Halifax's third five minutes later.
Hamilton finished well to make it 3-2 with two minutes remaining and set-up a tense finish but the visitors held firm to book a third round tie with Guiseley.
1. Brighouse Town 2 FC Halifax Town 3
The cup tie was watched by a crowd of 250. Photo: Charles Round
2. Brighouse Town 2 FC Halifax Town 3
The win gave Halifax a place in the third round where they faced Blue Square North rivals Guiseley. Photo: Charles Round
3. Brighouse Town 2 FC Halifax Town 3
Brighouse hit the woodwork as they battled back. Photo: Charles Round
4. Brighouse Town 2 FC Halifax Town 3
Two goals in the opening 20 minutes gave the Shaymen a great start. Photo: Charles Round