The midfielder lashed home from Darren Anderton's pass during in our best spell at the start of the second half but celebrations were cut short by the linesman's flag.
Jermaine Jenas rubbed salt into the wounds by grabbing the winner in the last minute.
Replays later showed that Gus was at least level when he received the ball and the goal should have stood.
Boss Glenn was in no doubts. "It was definitely onside," he declared. "I thought that during the game and I've now watched it back on our laptop in the dressing room and to me it's not even a difficult decision.
"It has cost us big time. It changed the complexion of the game and I believe it affected us as well, because we had a stranglehold on the game.
"We weren't at our best, didn't have enough creativity for my liking, but we came out of the traps in the second half, upped a gear, played with more guile and that goal came at the perfect time for us.
"If we'd have gone 1-0 up I'm sure we would have gone on to win from there so to have it chalked off, well, I can't explain how disappointed I am.
"Then we gave the goal away right at the death and we deserved better than that."
Glenn Hoddle couldn't hide his disappointment after Gus Poyet's 'goal' was ruled out in last night's late defeat against Newcastle.