Arjen Robben was adjudged to have been tripped in the area by Rafa Marquez in the injury time and Huntelaar coolly placed a brilliant penalty into the bottom-left corner to knock Mexico out of the tournament.
However, it was Wesley Sneijder who rescued the 2010 runners-up, in the 88th minute, bringing up the equaliser, cancelling out the 48th minute brilliant goal by Giovani Dos Santos which had put Mexico ahead.
Mexicans had dominated the match and looked destined to reach their first quarter-finals since 1986 but Sneijder's effort two minutes from time and Huntelaar's penalty in added time crushed their dreams.
Playing in the knockout stages for a sixth straight World Cup, Mexico dominated the proceedings right from the start and had four shots at the target in the first half itself but none of them enough to put them ahead.
Herrera came close early on after being fed by Peralta but his effort went wide of the bottom-left post, while a long shot by Salcido was easily parried away by Cillessen.
Holland, who struggled to keep possession early on, got a decent chance in the 28th minute when skipper Robin Van Persie, who is returning into the team after a suspension, brought a lofted ball down in the penalty area but he failed to connect properly as his right-footed effort went wide.
Mexico tested the Dutch backline once again in the next minute when Santos played a pass into Peralta, who received the ball and fired it at Cillessen from 25 yards.
In the 42nd minute, Mexico had another opportunity when Santos raced into the rival box and found Andres Guardado's pass but his acute angle shot was blocked by Cillessen.
In the stoppage time, Holland got a rare chance when Van Persie pounced on the ball after a lapse by the Marquez and raced towards the penalty area with Arjen Robben in support but the Bayern Munich winger played it late.