Guernsey levelled things up when Ross Allen laid the ball off for Matt Loaring to score eight minutes later.
It was Loaring’s 90th goal for the club.
But shortly afterwards another looping corner caused problems for GFC, a scramble on the line and a goal was given.
Guernsey FC are second from bottom in Isthmian South-Central.
Their next match is away to bottom club Binfield on Saturday 23 December.
Northwood: 1 Roraigh BROWNE; 2 Harry McKENNA; 3 Deago DUNBAR-BONNIE; 4 Luke TINGEY; 5 Romario JONAS; 6 Harry GALLAGHER; 7 Carl STEWART; 8 Teddy STACEY; 9 Godlove OPPONG (14 Reece CAMERON, HT); 10 Sam JENKINS (15 Keagan COLE, 85’); 11 Kofi ANOKYE-BOADI. Not used: 12 Zeid HANNACHI; 16 Harry McCORKELL.
Booked: Jenkins.
Guernsey FC: 1 Josh ADDISON; 2 Niall HAINSWORTH; 3 Dave MERRIS; 4 Tom DODDS; 5 Tom VAUDIN; 6 Seb VANCE (15 Keene DOMAILLE, 77’); 7 Charlton GAUVAIN; 8 Dave RIHOY; 9 Owen WALLBRIDGE; 10 Ross ALLEN; 11 Matt LOARING. Not used: 12 Joe Alvarez; 14 Brandon WALLACE.
Booked: Gauvain.