Twenty minutes into the match, Honduran goalkeeper Denis Escobar clattered into defender Bailey Wright after the Australian ventured forward for a set piece.
Replays showed the Bristol City captain judged his run perfectly to get onto Matthew Jurman's header, only to head over the bar under pressure from the opposing keeper.
Referee Daniele Orsato considered the clash and pointed to the spot, before incensed Honduran defenders made a bee-line for the linesman, claiming Wright had strayed offside.
Orsato then discussed the incident with his linesman and reversed his decision, elating the 40,000 strong home crowd.
Coach Ange Postecoglou looked puzzled on the sideline and still didn't understand the outcome after the match.
"I thought the referee paid a penalty and the linesman paid offside," he said.
"I asked the referee at halftime and he said, no, the linesman paid a goal kick.
"I was scratching my head because if it was a goal kick it would have meant Bailey got cleaned up."
Jedinak was given a different explanation.
"He blew for a penalty then he went to consult with the linesman ... came back and flagged for offside," the Australia captain said.
"It was quite quick.
"I don't have the benefit of a replay. It is what it is. You've got to accept it and go on."
Like his captain, Postecoglou was accepting of the verdict.
"Decisions happen and we cop that," he said.
"The ref did a good job. It was a hard game to referee."