Halifax looked to have the game won when they led 18-8 thanks to tries from Paul Handforth, Ben Heaton and Steve Tyrer, who also kicked three goals.
But the visitors lost their inspirational captain Scott Murrell to injury and Batley, who had led 8-6 at half-time thanks to Paul Mennell's try, seized their chance to snatch a share of the spoils.
Left winger Gareth Potts raced over for an 80-metre interception try and right winger Jonny Campbell dived over at the other corner in the final minute, with Tom Hemingway landing the touchline conversion.
