Fatih Terim's men needed to beat the Group D winners, who sealed their place in Brazil last week, while hoping rivals Romania dropped points.
But an early free-kick from Arjen Robben beat Volkan Demirel to put Turkey firmly on the back foot and Wesley Sneijder's goal shortly after the break confirmed a fateful 2-0 win.
It was a ninth win in 10 qualifying games for Holland but Turkey finished a poor fourth behind Romania and Hungary after both nations won their respective games against Estonia and Andorra.
In a game which featured a Holland side fresh from hammering Hungary 8-1 and a Turkey team desperate to secure second place, it was remarkable that the first 20 minutes produced only one shot on goal.
That solitary strike resulted in a goal for Holland.
In the eighth minute, Hasan Ali Kaldirim felled Robben as he loped towards the penalty area and the Bayern Munich winger promptly showed his gratitude by firing home the resulting free-kick.
His left-footed effort bounced once in front of an embarrassed Demirel before hitting the back of the net.
In the 21st minute, Robin van Persie got in the way of team-mate Sneijder's snapshot and seven minutes later Turkey enjoyed their first sight on goal.
Ajax goalkeeper Jasper Cillessen coped well with Arda Turan's effort and Holland raced straight down the other end, only for Jeremain Lens to blast Robben's cross over the bar.
Turkey pushed back, Semih Kaya unlucky not to test Cillessen with a header before Ron Vlaar blocked a smart strike from Burak Yilmaz.
It was the visitors who ended the first half on a high, though, Robben and Sneijder both slamming shots just wide of the mark.
And, immediately after the restart, the Galatasaray star hurt his host city with the second goal of the night.
Dirk Kuyt had replaced Van Persie in a double half-time substitution - Jeffrey Bruma taking over from Bruno Martins Indi - and the Fenerbahce man soon picked out Sneijder for an easy finish at the far post.
Ali Kaldirim opened Turkey up to further punishment with another foul on Robben but Sneijder's free-kick was parried clear by Demirel.
The Fener keeper was less happy to see Lens bearing down on him in the 55th minute but managed to tip the winger's clever lob over the bar.
He repeated the trick against Sneijder and Turkey were soon in the ascendancy.
Gokhan Tore led the charge, forcing a fine save from Cillessen before Vlaar and Daley Blind blocked efforts from Arda and Olcay Sahan.
Moments later, Cillessen tipped a swerving drive from Selcuk Inan into the crowd.
Holland had weathered the storm but they were caught cold in the 83rd minute as substitute Cenk Tosun snuck into the six-yard box to shave paint off the bar with a header.
Three minutes from time, Tosun appeared in the box once again to nod over, but Turkey's World Cup dream was over.