Media playback is not supported on this device
Former captain Aaron Hughes won his 100th cap as a 30th-minute substitute for defender Craig Cathcart who hobbled off injured after being fouled.
Cathcart was one of several players on the receiving end of tough tackles.
Visiting keeper Michael McGovern made some fine saves while Kyle Lafferty had a penalty claim turned down.
Lafferty felt his shot had been blocked by Peter Pekarik's arm, but referee Marian Radu Petrescu did not see it as a spot-kick.
Robert Mak came the closest to scoring for the hosts only to be denied by Hamilton stopper McGovern who was quickly off his line, while Martin Skrtel almost scored a late own goal following a Paddy McNair cross.
The Liverpool defender diverted McNair's driven cross towards his own goal, and keeper Matus Kozacik was forced into a save.
Northern Ireland open their Euro campaign on 12 June against Poland in Nice, the day after Slovakia meet Wales in Bordeaux.
One of Northern Ireland manager Michael O'Neill's chief concerns was to see his players come through unscathed with the opening Euro 2016 game against Poland just eight days away.
Worryingly for him, several key men were on the receiving end of some hefty challenges.
Media playback is not supported on this device
Gareth McAuley and Jonny Evans picked up minor knocks before the other man in the back three, Watford defender Cathcart, had to limp off after being fouled.
That led to 36-year-old Hughes coming on to win his 100th cap as a 30th-minute substitute.
It had been expected the former Newcastle and Aston Villa man would come one at some point for his landmark appearance, but O'Neill was forced to make the change earlier than planned.
As well as Cathcart, O'Neill will await a fitness update on striker Lafferty who came off in the second half with a leg injury.
Manager O'Neill deployed his favoured 3-5-2 formation, setting the team up in the way he will want them to play against Poland.
Paddy McNair caught the eye again in a wide role on the right while Millwall's Shane Ferguson came into the team to stake his claim for a starting role in Nice.
They appear to be competing with Conor McLaughlin and the absent Stuart Dallas for selection.
Any lingering doubts on who will be NI's first-choice keeper will have been ended by another solid display by McGovern.
The Northern Ireland squad head to their Lyon base on Sunday in good heart and with that record unbeaten sequence.
It was another outstanding defensive performance against a Slovakian side which had had defeated world champions Germany on 29 May.
Match ends, Slovakia 0, Northern Ireland 0.
Second Half ends, Slovakia 0, Northern Ireland 0.
Corner,  Northern Ireland. Conceded by Martin Skrtel.
Offside, Slovakia. Patrik Hrosovsky tries a through ball, but Vladimir Weiss is caught offside.
Substitution, Northern Ireland. Conor McLaughlin replaces Patrick McNair.
Corner,  Slovakia. Conceded by Gareth McAuley.
Attempt saved. Vladimir Weiss (Slovakia) right footed shot from outside the box is saved in the bottom left corner.
Substitution, Northern Ireland. Lee Hodson replaces Shane Ferguson.
Attempt blocked. Ondrej Duda (Slovakia) right footed shot from outside the box is blocked.
Attempt missed. Miroslav Stoch (Slovakia) left footed shot from outside the box is close, but misses to the right. Assisted by Dusan Svento.
Substitution, Slovakia. Adam Nemec replaces Juraj Kucka.
Substitution, Northern Ireland. Corry Evans replaces Oliver Norwood.
Offside, Slovakia. Vladimir Weiss tries a through ball, but Peter Pekarík is caught offside.
Attempt blocked. Miroslav Stoch (Slovakia) right footed shot from outside the box is blocked. Assisted by Marek Hamsik.
Corner,  Slovakia. Conceded by Aaron Hughes.
Corner,  Northern Ireland. Conceded by Jan Durica.
Attempt missed. Vladimir Weiss (Slovakia) right footed shot from outside the box is close, but misses to the left. Assisted by Dusan Svento.
Corner,  Slovakia. Conceded by Gareth McAuley.
Attempt blocked. Marek Hamsik (Slovakia) left footed shot from the right side of the box is blocked. Assisted by Miroslav Stoch.
Juraj Kucka (Slovakia) wins a free kick in the defensive half.
Foul by Shane Ferguson (Northern Ireland).
Attempt missed. Juraj Kucka (Slovakia) right footed shot from outside the box misses to the right.
Ondrej Duda (Slovakia) wins a free kick in the attacking half.
Foul by Oliver Norwood (Northern Ireland).
Attempt missed. Ondrej Duda (Slovakia) right footed shot from the right side of the box is too high. Assisted by Peter Pekarík with a headed pass.
Substitution, Slovakia. Ondrej Duda replaces Michal Duris.
Substitution, Slovakia. Miroslav Stoch replaces Robert Mak.
Martin Skrtel (Slovakia) wins a free kick in the defensive half.
Foul by Josh Magennis (Northern Ireland).
Offside, Slovakia. Jan Durica tries a through ball, but Juraj Kucka is caught offside.
Corner,  Slovakia. Conceded by Patrick McNair.
Offside, Northern Ireland. Michael McGovern tries a through ball, but Conor Washington is caught offside.
Foul by Juraj Kucka (Slovakia).
Oliver Norwood (Northern Ireland) wins a free kick on the left wing.
Corner,  Northern Ireland. Conceded by Peter Pekarík.
Attempt saved. Conor Washington (Northern Ireland) right footed shot from the left side of the box is saved in the bottom left corner. Assisted by Aaron Hughes.
Corner,  Northern Ireland. Conceded by Martin Skrtel.
Foul by Jan Durica (Slovakia).
Josh Magennis (Northern Ireland) wins a free kick on the right wing.
Delay over. They are ready to continue.
Northern Ireland will go into Euro 2016 on the back of a record 12-match unbeaten run after drawing away to fellow finalists Slovakia in Trnava.