Northern Ireland's slim hopes of Euro 2012 qualification are over after Estonia came from a goal down to secure victory at Windsor Park.
Steven Davis reacted quickest to fire home from Kyle Lafferty's low right-wing cross in the 21st minute.
But Konstantin Vassiljev's late brace - the first from the penalty spot - gave Estonia the win.
Northern Ireland have won just twice in 23 games and fans called for manager Nigel Worthington to leave his role.
The first chance of the game fell to Tarmo Kink in the ninth minute but his 20-yard left-foot shot was pushed round the post by Lee Camp.
Northern Ireland controlled large periods of the first half and were almost rewarded for their early superiority in the 15th minute, but Grant McCann saw his left-foot strike palmed away by Sergei Pareiko.
Davis opened the scoring when Lafferty crossed and the Rangers midfielder was first to the ball after Pareiko could only parry the ball.
For Davis, it was his fourth international goal on the occasion of his 50th cap.
Pareiko showed better handling skills to hold onto Pat McCourt's fizzing effort and Gareth McAuley had his shot blocked after going on a marauding run from defence.
Estonia looked sharper after the break, Camp saving well from Kink and then Sergei Zenjov beating the offside trap but firing wide with only the home goalkeeper to beat.
Soon after, Lafferty earned a yellow card for leading with his arm, a booking which rules him out of his side's final qualifier against Italy.
Substitute Corry Evans headed over the bar as Worthington's men sought the second goal which should have made the three points safe.
The visitors responded and Enar Jaager almost levelled in the 71st minute but the midfielder skewed his shot just wide after meeting a corner.
Zenjov then unleashed a left-foot drive but Camp was equal to the task.
Estonia deservedly equalised in the 76th minute when Craig Cathcart tugged at the shirt of Vassiljev inside the area and the striker picked himself up to score from the penalty spot.
Vassiljev grabbed his second with a stunning 30-yard shot into the top corner with six minutes remaining.
The referee's assistant put his flag up for offside but German referee Manuel Grafe waved play on and Vassiljev found the net, with the Northern Ireland defence static.
The result heaps further pressure on under-fire manager Worthington as his side boast just nine points from nine qualifying games so far.
Northern Ireland: Camp, Hodson, Cathcart, McAuley, Baird, Clingan, Davis, McCann, Lafferty, McCourt, Brunt.
Subs: Taylor, McGivern, C Evans, Healy, Feeney, McGinn, Little.
Estonia: Pareiko, Piiroja, Klavan, Jaager, Stepanov, Kruglov, Dmitrijev, Puri, Vunk, Kink, Ahjupera.
Subs: Londak, Reintam, Zenjov, Purje, Vassiljev, Saag, Teniste.