With neither side competing at the 2018 World Cup, interim manager Malky Mackay named a youthful, experimental lineup for the hosts.
The 45-year-old picked Celtic starlet Kieran Tierney as his captain for Scotland's first match at Pittodrie since 2013.
The hosts were quickest out of the starting blocks, with Matt Phillips and James Forrest seeing efforts charged down by the Dutch backline early on.
The visitors were kept at bay for the most part but managed to take the lead in the 40th minute when Scotland were left exposed at the back following an attack.
Scotland continued to impress going forward after the interval and John McGinn's 25-yard shot curled the wrong side of the post after a good passing move.
Cummings also had a great chance after coming on as a sub with his first touch, but Cillessen saved easily and the Dutch were able to see the game out to claim victory.