After world number one Novak Djokovic had continued his march through the draw to set up a mouth watering semi-final against Andy Murray, Nadal ran out of steam against the aggressive Klizan who won 6-7(7) 6-4 6-3 for the biggest scalp of his career.
Women's top seed Serena Williams was forced to pull out through injury while Maria Sharapova destroyed Svetlana Kuznetsova in an all-Russian women's quarter-final.
American world number one Williams, who had reached the last eight on the Beijing hard courts with a three-set win over Czech Lucie Safarova late on Thursday, cited a problem in her left knee for handing a walkover to Australian Sam Stosur.
It was the second tournament in a row the 33-year-old, who won her 18th grand slam singles title at the U.S. Open last month, had been forced to withdraw after she quit her opening match at the Wuhan Open last week because of illness.
Djokovic, looking for a fifth title at the China Open, dismantled a flat Grigor Dimitrov 6-2 6-4 in a one-sided quarter-final while Murray maintained his quest to qualify for the ATP World Tour Finals when he stormed past U.S. Open champion Marin Cilic 6-1 6-4.
Nadal, making his return from a wrist injury at the China Open having not played since losing at Wimbledon, seemed to be on course for the semis and a match-up with Czech Tomas Berdych when he edged the first set on a tiebreak.
At the scene of his 2008 Olympic gold medal Nadal was then a break ahead in the second set when the match began to turn in favour of 56th ranked qualifier Klizan.
Klizan broke the Nadal serve twice to level the match but Nadal again forged ahead in the decider, leading 3-2 with a break before the match slipped irreversibly out of his control.
Looking a little weary, the 28-year-old Nadal lost his serve to love and with Klizan playing a fearless brand of attacking tennis the Mallorcan suddenly found himself 5-3 down.
Klizan showed no nerves and finished the two hour 37 minute contest with a spectacular smash.
Earlier, Djokovic extended his winning run on the blue hardcourts of the National Tennis Centre to 22.
The Serb targeted the faltering backhand of the fifth seed in the opening set, which he took with breaks in the fourth and eighth games in an improved display after showing signs of rust in his opening matches.
Dimitrov showed more fight in the second set, breaking back with a thumping forehand cross court winner only to lose serve again in the next game to trail 4-2.
He broke again with a stunning backhand winner when Djokovic served at 5-3, but he could not capitalise and crumbled in the following game, ending the match with his third double fault.
Djokovic will face Murray, who, like Dimitrov, is chasing a place in the season-ending ATP World Tour Finals.
Murray, eyeing back-to-back titles after Sunday's Shenzen Open triumph, was far too good for Cilic, whose serve crumbled under pressure in the opening set.
In the women's tournament, Stosur will take on Wimbledon champion Petra Kvitova in the semis after the Czech beat Italian Roberta Vinci 7-6 (7) 6-4.
French Open champion Sharapova crushed Kuznetsova 6-0 6-4 in an hour and 24 minutes to set up a semi-final clash with former world number one Ana Ivanovic.
(Reporting by Patrick Johnston in Singapore and Martyn Herman in London; editing by Amlan Chakraborty and Toby Davis)
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