Northern Ireland's manager Sammy McIlroy was full of praise for his side after they came within three minutes of a most unlikely draw in Teplice.
The Irish team were severely under strength with 10 players injured or suspended against the side ranked seventh in the world and were undone only by two late goals from Pavel Kuka and the substitute Milan Baros.
"Everyone gave me 100 per cent commitment and I thought the defence in particular was absolutely magnificent," said McIlroy.
The Czechs broke through six minutes before half-time in controversial circumstances. Manchester United's former winger Karel Poborsky slipped the ball through to Kuka, who looked at least two yards offside, and as the defence stopped dead, the Slavia Prague striker placed the ball past Mark Taylor.
But the Irish responded with a superb strike of their own in first-half injury time. Ian Nolan started the move and Michael Hughes fed the striker David Healy, who crossed an inch-perfect ball to the back post for Philip Mulryne to nod in from close range.
The Czechs began the second half in dominant mood but were frustrated by dogged Irish defending. However, in the dying stages Kuka scored his 29th international goal when he stretched out a leg at the back post to convert Tomas Rosicky's flick on from Tomas Repka's corner.
Seconds before the final whistle Baros beat Nolan to the ball, cut inside and shot across Taylor, giving the Fulham keeper no chance.
In Copenhagen, Denmark scrambled to a late 2-1 win over minnows Malta to take over top place in the group from Bulgaria, who were held to a 1-1 draw in Iceland.
CZECH REPUBLIC: Srnicek, Repka, Votava (Bejbl 46), Tyce, Galasek, Rosicky, Nedved, Poborsky (Lokvenc 82), Berger, Kuka, Koller (Baros 64). Subs not used: Cerny, Ujfalusi, Smicer, Jankulovski. Goals: Kuka 39, 87, Baros 89.
NORTHERN IRELAND: Taylor, Aaron Hughes, Mark Williams, Murdock, Nolan, Michael Hughes, Griffin, Johnson (Ferguson 76), Mulryne (Kennedy 82), Elliott (James Quinn 66), Healy. Subs not used: Carroll, McCartney, Toner, Holmes. Booked: Griffin, Murdock, Aaron Hughes, James Quinn. Goal: Mulryne 45.
Referee: L Sundell (Sweden).
