With the game deep into injury-time Gulls defender Nicholson, who signed a new deal earlier this week, followed up his own long throw-in and fired a fine left-foot shot into the top corner.
Both sides hit the post in a frenetic first half on a wet and pacy Plainmoor surface. Eunan O’Kane was first to come within inches of breaking the deadlock in the 37th minute.
O’Kane sped away down the right and his right-foot shot from an acute angle beat Barnet keeper Dean Brill but smashed off the far upright.
Barnet then struck the post just before half-time as the Gulls failed to clear their lines in a goalmouth scramble. Bees skipper Mark Hughes seemed to get the last touch as the ball sped past home keeper Bobby Olejnik and smashed off the foot of the upright.
Torquay pressed in the second-half and with time running out, substitute Ian Morris had a header cleared off the line before Nicholson’s dramatic winner.