The Scots followed their 6-0 friendly thrashing by England with a disappointing second half in Nijmegen.
But the game could have been so different for Scotland if Tony Watt, Stuart Armstrong and Ryan Fraser had taken first-half chances as Scotland started brightly against a side they took four points from in the previous qualifying campaign.
Holland took the lead early in the second period through Tonny Trindade de Vilhena and the game ran away from Scotland midway through the half when they fell further behind moments after Stuart Findlay had headed against the post.
Billy Stark then looked on in horror as Luc Castaignos, Mike van der Hoorn and substitute Jesper Drost ensured the Dutch exacted revenge for their 2-1 defeat to the Scots in the same Goffertstadion less than two years ago.
Stark made four changes to the team that struggled so badly at Bramall Lane, half of them in defence where Hearts pair Kevin McHattie and Brad McKay dropped out.
Their replacements were both 17-year-olds making their debuts - another Hearts player, Jordan McGhee, and Celtic centre-back Findlay. The injured Stuart Bannigan missed out along with Islam Feruz, who was rested from the squad, with Jason Holt and Fraser coming in.
Scotland, who beat Luxembourg in their opening qualifier, were determined to atone for their embarrassment in Sheffield and Fraser twice came close in the opening 10 minutes. The Bournemouth winger first shot wide and then just failed to connect at the back post, with Dylan McGeouch involved in both moves.
Armstrong had a shot held before Watt forced a better save from Warner Hahn, with the rebound almost going in off a defender.
Jordan Archer made a decent save midway through the half but still Scotland came forward, with Armstrong failing to convert Findlay's header across goal.
Archer saved well from Quincy Promes before Armstrong had an even better chance to open the scoring when he burst through on goal, but the Dundee United midfielder fired over with only Hahn to beat.
Scotland were made to pay for their misses in the 52nd minute when Feyenoord midfielder Trindade de Vilhena lifted the ball over Archer following some Dutch pressure.
And the game turned firmly against them following a crucial passage of play midway through the half. Fraser had another chance when his former Aberdeen team-mate Ryan Jack played him through but his shot was blocked by the foot of Hahn.
Findlay soon crashed a header off the post from McGeouch's corner and Holland were two up within 120 seconds as Castaignos rifled past Archer in the 69th minute.
The goal sparked a collapse and five minutes later Ajax defender Van der Hoorn headed home from a corner.
Lewis MacLeod and Callum Paterson came on but Scotland fell further behind in the 78th minute when Castaignos set up Drost as Scotland conceded their 10th goal in two games.