The Danish marksman is keen to explore options in the summer which might involve a move home to his native country, while Cobblers boss Stuart Gray is keen to strengthen his pack for next season.
There was no masking Huberz's delight when he headed in the 69th minute free-kick from Daniel Jones which allowed the Cobblers to leapfrog Tranmere in the final League One table and finish in ninth position.
The home side had gone in front as early as the third minute when another Jones set-piece had only been partially cleared by the Rovers defence and Adebayo Akinfenwa pounced on the loose ball to beat Danny Coyne from close range.
Northampton had chances to extend their lead, although Robbie Stockdale might have equalised when his angled drive was tipped over the crossbar by 20-year-old Chris Dunn, who was making his league debut.
Anthony Kay wasted a great chance when he volleyed over a cross from Shane Sherriff.
Tranmere equalised two minutes before half-time with Chris Greenacre's 14th goal of the season.
The former Manchester City striker, who once spent a spell on loan at Sixfields, executed a superb free-kick after a corner was only half cleared and Paul McLaren headed the ball back into the danger zone.
Northampton almost regained their lead with Hungarian defender Gabor Gyepes seeing a stooping header well saved by Coyne, while Jones curled a free-kick just wide of the target.
Hubertz replaced Giles Coke in the 54th minute and his winner prompted wild excitement.
But the finale took on an ugly edge when Tranmere skipper Ian Goodison was sent off ten minutes from time for a second bookable offence after tangling with home midfielder Ryan Gilligan.