Sven Goran Eriksson's men never got their game plan off the ground and had to pull back one-goal deficits on two occasions in the first half to save even more embarassment.
David Seaman and Sol Campbell will come in for very harsh criticism as their mistakes brought two fine goals from the Macedonians, who celebrated a famous point in front of a stunned south coast crowd.
England's nightmare evening saw Steven Gerrard forced to leave the match on a stretcher with a serious leg injury in the second half while Alan Smith was foolishly sent off in injury time to add more misery to a woeful Three Lions performance.
The match started in a very slow fashion which would eventually bring an ominous set of events thanks to the efforts of an eager away side.
Macedonia then stunned the St. Mary's Stadium crowd on eleven minutes when a brilliant in-swinging corner from Sakiri flew over the head of David Seaman and went in off the inside far-post with Paul Scholes caught ducking and letting the ball go into the net to give the Balkan nation a shock 1-0 lead.
But as thoughts of a disaster beckoned, England captain David Beckham came up with a beautiful lob to level things on fourteen minutes.
Macedonia lost possession inside their half allowing Paul Scholes to play his Manchester United team-mate in and with goalkeeper Petar Milosevski off his line, Beckham measured his lob perfectly over his head to equalise.
The match settled down again but only server to bring a calm before another storm for the home side.
With Macedonia playing like they had not read the script, they stunned the Southampton crowd with a sublime second strike.
Sakiri hit a daisy-cutter ball from the left in England's half that hit Campbell in the legs in England's penalty box.
The ball came back nicely to Vanco Trajanov, whose deliberately placed right-foot finish took advantage of the unsighted Seaman, and put Macedonia back in front at 2-1.
England started to show some real urgency after the second goal and started to push Macedonia back again with some level of desperation.
Scholes then missed a decent chance when he ballooned a shot over Macedonia's bar from a goal-mouth scramble and Smith tested Milosevski with a solid shot on target, forcing the Macedonian goalkeeper into a low save.
However, England remained resilient and equalised nine minutes before half-time with an excellent Steven Gerrard volley.
Beckham swung in a corner from the left and after Macedonia failed to clear their lines, a header from the by-line by the England captain found the Liverpool midfielder, whose strike, after controlling the ball on his chest, gave Milosevski no chance.
In the second half, England continued to venture forward and following a ball played into the box, Gerrard tried a difficult lob that just went over Macedonia's bar.
Owen's performance had been quiet to this point but he was able to make a surging run in on goal that forced Milosevski to make another desperate save and as the ball was partially cleared, Ashley Cole screamed a volley across the face of goal into touch.
With only ten minutes gone in the second half, England suffered a major blow when the lively Gerrard went down with an injury and he had to be stretchered off looking in considerable pain.
Eriksson's men were showing mounting concern and were unfortunate when Owen scored a dubiously disallowed goal and Smith forced a save with his fine turn and shot in the box.
England went closer still when a corner gave Butt a chance but his shot was blocked off the line and the ensuing corner gave Smith another chance with a slicing volley that was always going wide.
With eight minutes to go, England won a free-kick just outside Macedonia's penalty allowing skipper Beckham to fashion one of his famous set pieces.
However, thought of the dramatic late goal against Greece were ended when Milosevski was in the right place to make an easy stand-up save from the Manchester United man's shot.
Vassell then went close with a great chance when Gary Neville crossed from the right but the Aston Villa man fired wide when he should have hit the target.
The spritely striker then nearly fashioned a winner when his cross in the box found the lively Smith, but his volleyed strike found the chest and arms of Milosevski.
The home side's frustration would bring a sending off in the five minutes of injury played when Smith - on a yellow for an earlier challenge - stupidly took out his marker with the ball going into touch.
Spanish referee Arturo Dauden Ibanez had no choice but to hand a second yellow card and dismiss the Leeds United firebrand from the closing stage and the final whistle brought boos from the crowd and deserved delight from the unfancied Macedonians.
Meanwhile, Turkey continued their fine run in their Euro 2004 qualifying campaign with an easy 5-0 win over minnows Liechtenstein at the Ali Sami Yen Stadium in Istanbul.
Galatasaray's home ground provided the backdrop for another likely Turkish success but it was the away side that went closest to scoring first when striker Mario Frick tried to lob Turkish goalkeeper Rustu Recber, but his effort went just wide.
The Turks then took control when Okan Buruk finished right-footed from a short pass at the top of Liechtenstein's box to make it 1-0 after six minutes.
They home side made it two inside a quarter of an hour when Umit Davala headed between goalkeeper Peter Jehle's legs after a fine cross from the right.
Ilhan Mansiz made it three with a volley from six yards after Liechtenstein failed to clear an Arif Erdem cross.
Senol Gunes' men created more chances to further increase their lead before the break, as they controlled most of the play through midfield.
Frick remained Liechtenstein's only real threat, causing Recber to make a comfortable save just before half-time.
The second half saw Turkey pick up where they left off, controlling proceedings with Arif Erdem going closest to scoring with two big chances after the break.
But it was substitute Akin Serhat with two goals in the last eight minutes to seal another comfortable victory as Turkey go top of Group Seven with three wins from three matches.
Liechtenstein did receive a penalty in the last seconds but after spot-kick was saved, the referee cruelly blew for full-time as the away side slotted home the rebound, preserving Recber's clean sheet.
Click below England v F.Y.R. Macedonia match stats.
European Championship Group 7 qualifier
England 2-2 F.Y.R. Macedonia
For the Euro 2004 qualification tables click here
