In a game littered with defensive mishaps, woeful lapses in concentration from goalkeeper Lee Camp and defender Gareth McAuley were responsible for two of Estonia's four goals, with the consolation effort coming only when Raio Piroja put the ball past his own keeper.
Comprehensive defeat to a nation ranked 86th in the FIFA rankings - 27 spots below Northern Ireland - will hurt but, having lost to Serbia on Friday too, it also leaves them fifth in Group C and with no hope of salvaging a play-off spot.
David Healy was winning his 89th cap, a figure that lifted him to third on his country's all-time list, but he could not break a near three-year international duck in a match that will be remembered for his side's dismal exploits at the other end of the pitch.
With a strong travelling support of almost 1,200 and a noisy home crowd, the game started at a high tempo.
Northern Ireland looked nervy in the opening moments, Chris Baird and Steven Davis both finding touch with mis-cued passes.
Estonia's Sander Puri attempted to take advantage when he called for a penalty five minutes in, only for the referee to wave away his hopeful appeal.
With 10 minutes gone Niall McGinn got his side going, accelerating past two men after a neat flick on the right but his cross did not find Healy in space.
Davis, whose poor back pass had handed Serbia victory on Friday, looked a man with a point to prove and was by some distance his side's busiest player.
Grant McCann wasted an inviting free-kick from 25 yards as Northern Ireland settled and soon after narrowly failed to get a full connection on a back-post header.
Martin Vunk had looked dangerous when Estonia went forward and it was the midfielder who gave his side the lead after 28 minutes.
Dmitri Kruglov broke down the left flank, beating Baird before McAuley failed to deal with his low cross.
Instead, the ball deflected to the edge of the area, where Vunk was on hand to drill home.
Worse was to come four minutes later, Tarmo Kink shooting speculatively from distance only for Camp to produce his horror moment as the ball bounced just in front of him.
The Nottingham Forest goalkeeper appeared to misjudge the flight of the ball and as he tried to smother it with his legs, succeeded only in diverting it over the line.
Such was Northern Ireland's malaise that Puri next felt inclined to shoot from a free-kick nearly 40 yards out.
The hosts were not immune from errors of their own, though, and when Davis' 39th-minute free-kick was helped on by McAuley, Piroja contrived to head the ball into his own net.
Both defences were now looking at sea and only an offside flag denied Healy as he stooped to head in McGinn's cross just before the break.
Five minutes of the second half had passed when Healy, striving to reach a loose ball, went down as goalkeeper Sergei Pareiko dived to intercept.
Healy was up again seconds later appealing for a spot-kick but referee Daniel Stalhammar was unmoved.
Northern Ireland forced three successive corners as they attempted to leave Tallinn with something but the Estonian defence held firm on each occasion.
The same could not be said for Worthington's backline which gave up another shocking goal on the hour.
First Puri eased between Hughes and Craig Cathcart to head against the post, then McAuley dawdled after collecting the loose ball, allowing Sergei Zenjov to steal in behind him and rifle home from close range.
Camp miskicked under pressure again soon after as Northern Ireland's error count continued to soar.
Worthington sent on strikers Warren Feeney and Josh McQuoid with 25 minutes left, Healy and McGinn trudging off.
Zenjov almost added his second after turning McAuley as Northern Ireland looked increasingly ragged on the back foot.
Chris Brunt and McCann both made Pareiko work in the home goal but he was handed comfortable saves by both men.
McAuley was deployed up front in the last 10 minutes, potentially to make use of his height but possibly to end his disastrous day at the back.
Estonia looked to test the shellshocked Camp at every opportunity and a fourth goal came in injury time as the keeper palmed a deflected cross to Konstantin Vassiljev, who cut back for Kaimar Saag to convert.