On an evening when Goran Pandev made his 122nd and final appearance for the Macedonians, Wijnaldum scored twice inside seven second-half minutes to cement a win which had been set up by Memphis Depay's 24th-minute strike at the Johan Cruyff Arena.
The Dutch, who were already assured of top spot, will now head for Budapest and a last-16 clash with one of the best third-placed teams in Groups D, E or F on Sunday, while the tournament debutants will return home pointless, but certainly having made an impression.
North Macedonia showed plenty of early intent as they attempted to leave on a high.
Indeed, they had the ball in the net with just nine minutes gone when Ivan Trickovski ran on to Pandev's clever flick and fired past Maarten Stekelenburg, only for an agonisingly tight offside decision to end his celebrations.
Their luck did not improve with 22 minutes gone when Aleksandar Trajkovski - with Pandev once again the architect - beat Stekelenburg with a fine strike only to see it come back off the upright, and their dismay was to increase within seconds.
Daley Blind's challenge on Pandev left the striker in a heap, but sparked a blistering counter-attack at the end of which Depay exchanged passes with Donyell Malen before sliding the ball past Stole Dimitrievski to open the scoring despite a VAR check on Blind's contribution.
The Macedonian keeper kept his side in it with a save at the feet on Denzel Dumfries on the half-hour mark, and they might have been back on level terms before the break had defender Visar Musliu been able to better direct his header.
They would have been further behind, however, within five minutes of the restart had Trickovski not been perfectly-placed to clear Matthijs De Ligt's bullet header off the line, although the respite was temporary.
Only seconds more had elapsed when Wijnaldum timed his run to perfection to meet Depay's cross and extend Holland's lead, also ensuring their run of scoring two or more goals in consecutive games extended to 10.
And the game was effectively over with 58 minutes gone when, after Dimitrievski had palmed away Depay's effort, Wijnaldum followed up to make it 3-0.
Substitute Wout Weghorst rattled the crossbar seconds before Pandev was afforded a guard of honour by his team-mates as he was replaced by Tihomir Kostadinov with 21 minutes remaining.