In his first competitive game in charge, Liverpool boss Roy Hodgson left out 10 of his World Cup stars, including captain Steven Gerrard.
But Liverpool were comfortable, opening the scoring when Ngog lofted over the goalkeeper after a defensive mix-up.
Ngog's second was a cool six-yard volley from Martin Kelly's cross.
For Hodgson, the victory was vindication of his decision to leave most of his key players at home, a risky strategy considering the Europa League represents Liverpool's only hope of European glory this season.
Hodgson had criticised governing body Uefa for making Liverpool play a qualifying game only 18 days after the World Cup and left the likes of Gerrard, new signing Joe Cole, Jamie Carragher and Glen Johnson back in Liverpool.
Argentina duo Javier Mascherano and Maxi Rodriguez did not travel either, as well as Spain's Fernando Torres, goalkeeper Pepe Reina and Dutch forwards Dirk Kuyt and Ryan Babel.
But the patched up Liverpool team proved to have more than enough strength and guile to hold off an enthusiastic but limited FK Rabotnicki side, who should not pose any problem in the second leg at Anfield on 5 August.
From the start, Liverpool's game plan appeared to focus on being tight in defence and worrying about attack secondarily.
And with only half of the starting XI being first-team regulars it was perhaps telling that three of the experienced players called on were defenders, in Martin Skrtel, Daniel Agger and Sotirios Krygiakos - all of whom played in the World Cup group stages for Slovakia, Denmark and Greece respectively.
That defensive unit gave Liverpool the solid platform to build on as, after a slightly disjointed start, the Premier League side grew in confidence and controlled the game.
The only clear-cut chance of the first half produced the opening goal when captain Lucas chipped his free-kick towards the edge of the area for Ngog to chase.
The Frenchman was rewarded for his endeavour when goalkeeper Martin Bogatinov and Egzon Belica both missed the ball and he was left to comfortably lift his finish over the keeper.
Rabotnicki were limited to one first-half chance but Ze Carlos's long-range strike was easily collected by Brazilian compatriot Diego Cavalieri.
Liverpool often looked in cruise control in the second half with their main threat coming through the impressive Ngog.
The 21-year-old striker scored eight goals in 37 appearances for Liverpool last season, a return which could not make up for the loss of Torres for long periods through injury.
But the France under-21 international showed glimpses of real quality against the Macedonian side in a display which suggested he may be able to force his way into Hodgson's thinking this season.
Ngog's second goal came when he met Kelly's cross from the right with a neat volley on the edge of the six-yard box which flew into the top right corner.
Another striker on show for Liverpool was Milan Jovanovic, who signed on a free transfer from Standard Liege this summer.
But playing on the left of a front three for the most part, the Serbia international was unable to mark his debut with a goal.
Liverpool used much of the second half as a training exercise, with Hodgson throwing on youngsters Stephen Darby, Lauri Dallaa Valle and Nathan Eccleston as his first competitive game in charge went almost entirely to plan.
Argentina duo Javier Mascherano and Maxi Rodriguez did not travel either, as well as Spain's Fernando Torres, goalkeeper Pepe Reina and Dutch forwards Dirk Kuyt and Ryan Babel.
But the patched up Liverpool team proved to have more than enough strength and guile to hold off an enthusiastic but limited FK Rabotnicki side, who should not pose any problem in the second leg at Anfield on 5 August.
From the start, Liverpool's game plan appeared to focus on being tight in defence and worrying about attack secondarily.
And with only half of the starting XI being first-team regulars it was perhaps telling that three of the experienced players called on were defenders, in Martin Skrtel, Daniel Agger and Sotirios Krygiakos - all of whom played in the World Cup group stages for Slovakia, Denmark and Greece respectively.
That defensive unit gave Liverpool the solid platform to build on as, after a slightly disjointed start, the Premier League side grew in confidence and controlled the game.
The only clear-cut chance of the first half produced the opening goal when captain Lucas chipped his free-kick towards the edge of the area for Ngog to chase.
The Frenchman was rewarded for his endeavour when goalkeeper Martin Bogatinov and Egzon Belica both missed the ball and he was left to comfortably lift his finish over the keeper.
Rabotnicki were limited to one first-half chance but Ze Carlos's long-range strike was easily collected by Brazilian compatriot Diego Cavalieri.
Liverpool often looked in cruise control in the second half with their main threat coming through the impressive Ngog.
The 21-year-old striker scored eight goals in 37 appearances for Liverpool last season, a return which could not make up for the loss of Torres for long periods through injury.
But the France under-21 international showed glimpses of real quality against the Macedonian side in a display which suggested he may be able to force his way into Hodgson's thinking this season.
Ngog's second goal came when he met Kelly's cross from the right with a neat volley on the edge of the six-yard box which flew into the top right corner.
Another striker on show for Liverpool was Milan Jovanovic, who signed on a free transfer from Standard Liege this summer.
But playing on the left of a front three for the most part, the Serbia international was unable to mark his debut with a goal.
Liverpool used much of the second half as a training exercise, with Hodgson throwing on youngsters Stephen Darby, Lauri Dallaa Valle and Nathan Eccleston as his first competitive game in charge went almost entirely to plan.
