After reaching the knockout stages of Euro 2016, Northern Ireland went into the match on a high but they almost fell behind as early as the fifth minute in Prague when Pavel Kaderabek missed the target with a header.
Chances were few and far between as both teams tried to establish themselves in the contest, but it took until the 29th minute for the next clear-cut opportunity to be created as Paddy McNair saw his effort well saved by Tomas Vaclik.
Czech Republic had the better of the play during the closing stages before the break but a low effort from Northern Ireland's Stuart Dallas would represent the only shot on target as the half drew to a close.
The home side began the second half on top with Vaclav Kadlec firing a shot too close to Northern Ireland stopper Michael McGovern, before Filip Novak failed to make the most of an opening inside the six-yard box.
As the game entered the final quarter, Northern Ireland had what appeared to be a legitimate penalty shout turned down when David Pavelka seemed to handle the ball inside the area, and Czech Republic almost capitalised when Kadlec fired a rebound towards goal but it was blocked by a defender.
Ladislav Krejci could have won it for Czech Republic with a minute remaining of normal time, but after he failed to hit the target, Northern Ireland were able to hang on to secure what could prove to be an important point away from home.