Since beating the Faroe Islands 4-0 in August to raise hopes of securing a play-off place, Worthington's side have lost to Serbia at home and suffered back-to-back humblings at the hands of Estonia.
A 4-1 mauling in Tallinn was followed up by the 2-1 reverse at Windsor Park, with the visiting side having much the better of the play in a dominant second half.
Worthington's contract was due to expire at the end of the year, with Northern Ireland not due to play again after Tuesday night's match in Italy until next February.
He admitted his frustration at Northern Ireland's failure to qualify for the finals but refused to be too downbeat in the wake of the Estonia defeat.
"Of course there is frustration and yes I am disappointed (by results), but I try to look at the whole picture," he said at the weekend.
"You see what you have to work with, the numbers you have, the people who aren't there for one reason or another, but that's international football.
"You can't buy in, sell out or loan someone. You make the most of it and it's as simple as that. No excuses."
Former Northern Ireland international Michael O'Neill, currently steering Shamrock Rovers through a Europa League group stage, has been linked with the job while Lawrie Sanchez - Worthington's immediate predecessor - has said he would be keen to return to the post.
Worthington revealed the news at a press conference at the team hotel in Pescara, only minutes after informing the players of his decision.
With Irish Football Association president Jim Shaw watching on, Worthington said: "The situation is that as from (Tuesday night) I will step down as manager of the national team.
"Up until three games to go (in Group C) we were in a very good position but, through no-one's fault, sometimes the game of football throws you a raw hand.
"I feel the time has come after four and a half years, which have been fantastic for me as an individual.
"Sometimes when you try to get blood out of a stone there's only so much you can get. I think I've gone as far as I can with the group we've got."
Worthington, who has been subjected to some negative chants from the fans in the last two matches - defeats at home and away to Estonia - denied the supporters had influenced his decision.
"It wasn't difficult," he added. "I spoke to the IFA president (on Sunday night) to make him aware of my thoughts.
"It's not through supporter pressure because I can deal with that. It's a football decision that I think is right.
"The question was asked of me at the outset 'would I turn my back on my country?'. I said no then and I was determined to see it through and that is what I've done."
Worthington's assistant Glynn Snodin and goalkeeping coach Fred Barber will also step down.