Georginio Wijnaldum hit a double for the Netherlands after Memphis Depay opened the scoring on 24 minutes in the comprehensive win in Amsterdam.
However, Macedonia had their chances early, with Aleksandar Trajkovski having a goal disallowed, before hitting the woodwork too.
Donyell Malen raced forward to set up Depay for the opener, with the Olympique Lyon man laying off the pass for Wijnaldum’s goal on 51 minutes to make it 2-0.
Seven minutes later Wijnaldum, who signed with Paris Saint-Germain last week, netted another to seal the win.
Dutch boss Frank de Boer was delighted with Depay and Malen’s combination in attack, preferred ahead of Wout Weghorst.
“It looked good at times. Wout of course also wanted to play, but he expected me to try something different today,” he said.
“Whether we will do it again in the next game depends partly on the opponent. In any case, I think we have made progress in all aspects. At times it was a whirlwind and we are doing well.”
The Dutch will play third from either Group D, E or F in the last 16, while Austria are through to take on Italy.
Hoffenheim midfielder Chrstoph Baumgartner scored the only goal as Austria claimed a 1-0 win which qualified them for the knockouts in second spot ahead of Ukraine.
The defeat means Andriy Shevchenko’s side will need to wait to find out if they qualify for the next round as one of the four best-ranked third-place sides which seems unlikely with only three points from three games.