The teams were tied 4-4 at the end of regulation time but neither side could break the deadlock in overtime.
The game went into a tense shootout and the Admirals won 5-4.
The home side scored at its first attempt but missed its next two attempts.
The Stampede missed its first but scored the second, only to have the goal disallowed.
The officials, who had awarded the goal, reversed the decision after the Stampede player was judged to have taken the puck backwards.
The visitors missed their last attempt, handing the Admirals the win.
Stampede personnel reviewed the video footage after the game and were convinced the goal should have been allowed.
"We're very disappointed about it," Steve Rout told the Otago Daily Times.
"After looking at the video evidence, it is clear it was a goal."
Officials also came under scrutiny in Dunedin, where Thunder coach James van Leeuwen described the standard as below par.
His side upset the Botany Swarm 5-4 in overtime on Saturday, but produced a lacklustre display yesterday, losing 4-1.
"The refereeing is substandard. The calls that get missed both ways just get the teams agitated and fired up," van Leeuwen said.
"I don't think it cost us the game. It comes down to the players and we need to take responsibility.
"We should have come out stronger but the guys' hearts weren't in it and their heads weren't in it."
Ill-discipline also cost the Thunder.
Forward Damien Watson was expelled from the game for misconduct, after remonstrating with the referee.
The Stampede played the Admirals in the second leg of a double-header last night.
