Striker Hubertz helped haul his side back into the game after a first half in which Huddersfield were in total command.
Cobblers' boss Stuart Gray started with a defensive formation aimed at thwarting Huddersfield, getting 10 men behind the ball.
The Northampton defence was uncompromising in the driving rain and swirling wind and held Huddersfield until first half stoppage time.
With just seconds left, veteran Andy Booth was left unchallenged for the first time and he cashed in by heading home Andy Holdsworth's deep cross.
It was Booth's fourth goal in three games over the festive period and that should have been enough to set Huddersfield on their way to three points.
Booth had the chance to seal victory in the 56th minute when he collected a Phil Jevons flick on. He cleverly side-stepped a defender on the edge of the box but shot wide.
Gray switched to a 4-3-3 formation at half-time and they quickly began to get on top.
Huddersfield keeper Matt Glennon pulled off a fine double save when he denied Jason Crowe and then turned Andy Kirk's effort onto the bar.
Northampton levelled through Hubertz in the 71st minute after Bradley Johnson's header from a corner. Hubertz fired home from close range.
The Cobblers refused to be satisfied with a point and continued to press forward.
Five minutes from time Hubertz sent over a cross from the right for Crowe to drill into the bottom corner.