Rangers midfielder Steven Davis left their training base before the game and returned to his home in England to deal with a personal matter.
It was a blow for Nigel Worthington, given his side were facing a side ranked eighth in the world.
However, the province emulated England and achieved a gritty draw against the Czechs with a performance far more confident than the one at the weekend when they went down to Slovakia in Bratislava.
The downside was a shoulder injury to Norwich midfielder Sammy Clingan who did not appear in the second half.
There was a scare for Northern Ireland as early as the sixth minute when Marek Jankulovski delivered a free-kick from distance.
It seemed to be caught on the wind and goalkeeper Maik Taylor was happy to tip the ball over the bar.
The Czechs came close again three minutes later after Radek Sirl swung in a corner from the right.
Radoslav Kovac peeled away from his marker and headed narrowly over the bar to the province's relief.
Then Petr Cech did well to scramble the ball away in the 18th minute following a wayward header from team-mate David Rozehnal.
The Czechs responded and Taylor got down quickly to smother a shot from Libor Sionko.
David Healy had made a quiet start but sprung into action in the 23rd minute. However, his chip was too ambitious and Cech was able to take it with a degree of comfort.
Northern Ireland surged forward in the 33rd minute and Gillespie saw his effort cleared by Rozenhal.
However the Czechs launched another swift counter-attack a minute later, only for Jan Polak to send a shot high over the bar.
Healy was then left on the floor following a challenge by Polak and needed on-pitch treatment.
However to the relief of the supporters the Sunderland striker was able to resume his role in the team.
The Czechs broke forward in the 43rd minute but Sirl dragged his shot wide of the post.
Milan Baros should have put the visitors ahead on the stroke of half-time but headed wide following a cross from Zdenek Grygera.
Northern Ireland began the second half brightly and Cech did well to block Feeney's effort from an acute angle in the 51st minute.
The ball broke to Brunt on the edge of the area but he sent his effort high over the bar.
Then Brunt spotted Cech out of his goal and tried to lob him from distance but his ambitious effort went wide.
Then Tomas Ujfalusi was booked in the 63rd minute for taking a lunge at Healy as he tried to break forward.
This was a good spell by Northern Ireland and Gillespie rattled in a shot a minute later which was cleanly taken by Cech.
Gillespie was showing little sign of that ankle injury which had troubled him this season and was providing a good outlet on the right as the match entered a crucial stage.
Burnley striker Martin Paterson was then drafted into the action after 72nd minute when he replaced Warren Feeney.
Six minutes later Paterson got on the end of an inswinging cross from Brunt but headed wide of the post - although Northern Ireland secured a hard-earned draw.