The visitors came from a goal down and deserved their victory with a commanding second half performance but the result now leaves Worthington clinging to his job - and he knows it.
Some disgruntled fans called for Worthington to go at the finish as the reality of another failed attempt to make it to a major finals dawned.
And it could have been an even darker night for the hosts if goalkeeper Lee Camp had not performed more heroics.
Worthington, who must rally the troops for a daunting trip to Italy on Tuesday night, said he understood the fans' frustration.
"I'm frustrated and disappointed," he said. "In the first 45 minutes I thought we were excellent and good value for money. We created chances and got people forward.
"They came at us in the second-half and we had to make changes. The rest is history after that.
"The fans are as frustrated and disappointed as me. I look at the whole picture and see what I'm working with.
"That's the challenge of international football where you have got what you have.
"There are no excuses or hiding places, that's football. It's a fashionable thing for expectations to be high but I enjoy the game too much to take the enjoyment away.
"Nobody likes losing and the manner in which you lose can sometimes be challenged but I don't think it can be challenged tonight.
"As for my future, that's the million dollar question and what decisions people make is entirely up to them.
"I can't ask any more from the players, their effort and commitment has been first class.
"The spirit has been superb."
Northern Ireland were in the driving seat when Steven Davis, on his 50th cap, poked in the opener but Estonia's Konstantin Vassilijev conjured up a brace to steal the points.
The first goal was a penalty and the second was a stunning strike, though Northern Ireland claimed an offside. Their protests were in vain.
"My reaction was no different to the players," added Worthington.
"I saw the flag go up, I went for a drink of water and all of a sudden the ball's in the back of the net.
"There is no point in having people there to help if the referee isn't going to take notice of them.
"Anyone who watched the game can make their own minds up as to whether we got the decisions from the referee we deserved. The fourth official was as dumfounded as I was.
"I don't like moaning about referees. I'm focused on my players."
When asked how difficult it would be to raise his players for the Italy test, the former Norwich City boss added: "Ask me on Tuesday night and I'll give you an answer.
"They are a good group of players who have worked hard and hopefully we can put in a performance in Italy.
"It will be difficult. We have some hefty knocks. Sammy (Clingan) has a back spasm and that will need attention.
"Lee Camp has a groin problem which he had at half-time but credit to him, he wanted to carry on. Kyle (Lafferty) being out for Tuesday is a loss for us."
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