A deflected strike by Galatasaray forward Burak Yilmaz in the 37th minute handed the visitors the lead in the Dutch capital and looked set to inflict a damaging defeat on the hosts that would have increased the pressure on Netherlands coach Guus Hiddink.
However, Huntelaar's goal in the second minute of injury time allowed the Dutch to extend an unbeaten record on home soil in competitive matches stretching back to October 2000.
Nevertheless, they were unable to record a 20th consecutive home win and remain third in qualifying Group A halfway through the campaign, five points behind second-placed Iceland, who won 3-0 in Kazakhstan.
Only the top two in each group are certain to qualify for next year's finals in France, with the third-place finisher likely to go into a play-off.
As it stands the Netherlands, semi-finalists at last year's World Cup, have much catching up to do and also remain just two points better off than Turkey, who were unlucky not to hold on for the win.
The Oranje, who have not failed to qualify for a European Championship finals since 1984, were without injured stars Robin van Persie and Arjen Robben and struggled badly, deservedly falling behind eight minutes before the break.
Stefan de Vrij's poor headed clearance fell to Volkan Sen, who set up Yilmaz, and he rifled home right-footed with the aid of a deflection off Bruno Martins Indi.
The hosts trailed at the break despite boasting 76 percent of the possession and they continued to toil in front of goal after the restart.
Substitute Luciano Narsingh snatched at a great opportunity in the 54th minute, while Ibrahim Afellay had a long-ranger turned over and captain Wesley Sneijder crashed a free-kick just wide.
The game looked to be up until they equalised in the 92nd minute, a shot from Sneijder -- who plays his club football in Turkey for Galatasaray -- taking a decisive touch off Huntelaar and ending up in the net.
That came as a huge relief to Hiddink, who had an unsuccessful spell as coach of Turkey in their failed to bid to qualify for Euro 2012.
And it allowed Holland to extend an impressive record in Amsterdam, where their only previous competitive loss had come on penalties to Italy in the Euro 2000 semi-finals.