They were leading through Steven Davis' first-half strike until the 77th minute, before Konstantin Vassiljev scored twice in quick succession to take the points.
The first came from the penalty spot, with Craig Cathcart the guilty party, but the second was the one that infuriated the players.
It was a stunning strike from 30 yards but a linesman's flag had been raised in the build-up.
"It's difficult to take, it's frustrating, it's disappointing," said Worthington, whose hopes of a new contract took another blow today.
"There's a natural reaction (the winning goal). My reaction was no different to that of the players. I saw the flag go up, turned round to get a drink of water and all of a sudden the ball has hit back of the net.
"There's no point in having people there to help the referee if you're not going to take any notice of them.
"But I'm not one to moan about anybody. Everyone can make their own opinions about the referee."
Worthington was seen in conversation with the fourth official as his players protested against the 84th-minute strike, but he was unable to glean anything helpful from the exchange.
"He was as dumbfounded as I was, but it isn't going to change now so we move on," said Worthington.
Having been subjected to some negative chants following last month's 4-1 defeat in Tallinn, it was expected that Worthington would be given another rough ride by the fans.
There were a small number of banners and a portion of the crowd called for the manager's exit at the final whistle, but Worthington remained stoic.
"The fans are as frustrated and disappointed as I am," he said.
"It's the game and I've been in football long enough to get on with it. There's no excuses, no hiding places."
With just one more match left before the end of his current deal, a tough assignment against group winners Italy in Pescara on Tuesday, Worthington's future will be decided sooner rather than later.
Quizzed on his chances of taking charge of a third full campaign, he added: "I haven't got a clue. That's the million dollar question.
"A win is what myself and the players wanted. What other people make decisions on is up to them. I'm employed until December 31 and I've enjoyed the role.
"I'm working with a great group of players and you try and make the most of that group. I think over the course of this campaign we have."
Of more immediate concern to Worthington will be plugging some new gaps in his squad before flying to Italy on Sunday.
Frontman Kyle Lafferty, only just back in the side after injury, is suspended following his yellow card, while Sammy Clingan is a doubt after being forced off after half an hour with a back spasm.
Goalkeeper Lee Camp also has a knock, meaning there could be one final cap for veteran Maik Taylor on Tuesday.
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