The Tottenham midfielder's second-half effort alongside an early own goal set Van Marwijk and his team on their way to victory after a few troubling results ahead of Euro 2012
After two consecutive friendly losses to Bulgaria and Bayern Munich, Bert Van Marwijk's men made no mistake at the third time of asking, with an own goal from Kornel Salata putting them in control early in the first half.
Rafael Van der Vaart came off the bench to seal victory with a quarter of an hour to go to finally inject some positivity into Netherlands' Euro 2012 preparations, ahead of tough Group B matches against Germany, Portugal and Denmark.
Amid a raucous atmosphere at De Kuip, the hosts stormed into the lead after only eight minutes. Ibrahim Afellay was the instigator, drilling a low centre across the face of goal that was inadvertently turned in by Salata.
Netherlands could have added a second goal within minutes, but Robin van Persie fired off target after getting past Peter Pekarik.
Slovakia frequently came off second best as the first-half wore on, and were finding it increasingly difficult to cope with the technical superiority of the Dutch in midfield and attack.
However, they were handed a route back into the match just before the half-hour mark, when Maarten Stekelenburg inexplicably elected to pick up a back pass from defender Gregory van der Wiel.
Miroslav Stoch lined up the set-piece from just outside the six-yard box, but could only blast harmlessly into the side-netting.
The Fenerbahce winger went even closer to an equaliser moments later, when his effort from a tight angle rebounded off the post, following a swift counter-attack led by Marek Hamsik.
The flow of the match died down shortly after, with Netherlands unable to maintain their early promise in attack. They were nearly pegged back on the stroke of half-time, as Slovakia saw a couple of chances go begging.
First, a deep cross from Dusan Svento almost caught out Stekelenburg at the far post, but the Roma keeper did enough to tip it away from danger. Then, a long ball over the top released Marek Bakos through on goal, but his finish was smashed just wide across the face of goal.
Neither team seemed in any great hurry to force the issue coming out of the interval, with goalmouth action remaining elusive for much of the second half.
Netherlands were handed a chance to break the monotony with just under 20 minutes to go, after Van der Vaart was felled on the edge of the area by Marek Cech.
The Tottenham midfielder stepped up himself to take the free-kick, but saw a wonderful effort smack back off the frame of the goal, with Jan Mucha completely beaten.
Oranje went close again a few minutes later when Van der Wiel’s delivery flashed dangerously across goal, and somehow ended up in the arms of Mucha after a touch by Afellay.
They would eventually get their second, though, courtesy of a combination between two substitutes. Klaas-Jan Huntelaar appeared to have been blocked off by a pair of Slovak defenders inside the area, but did just enough to tee up Van der Vaart for a straightforward drive into the far corner.
Van Marwijk's side round off their Euro 2012 preparations with their final friendly match against Northern Ireland on Saturday at the Amsterdam Arena.