While holder Rafael Nadal of Spain and fourth-seeded Briton Andy Murray both advanced, second seed Djokovic was eliminated in a match lasting one hour and 44 minutes.
The Serbian world number two, winner here in 2008, lost his serve in the sixth game of the second set and sent a forehand service return long to hand Ljubicic victory. Ljubicic, the 20th seed, fired down 13 aces in the searing desert sunshine to record only his second win against Djokovic in seven meetings.
"I had a lot of opportunities and I didn't use many of them," Djokovic told reporters after converting only two of five break point chances. "My execution was very bad and he played well when he needed to."
Although the 6ft 4in (1.93m) Ljubicic lost serve in the third game of the match, he broke back in the eighth and 12th to take the opening set in just under an hour.
Booming serves
Repeatedly unleashing first serves above 130 mph, he swept through the second set to book a place in the quarterfinals against 21st seed Juan Monaco of Argentina, who beat Spaniard Guillermo Garcia-Lopez 3-6, 6-2, 6-1 earlier in the day. Djokovic's early departure followed the premature exit on Tuesday of world number one and three-times champion Roger Federer, who suffered a shock defeat to Cypriot Marcos Baghdatis.
Nadal overcame towering American John Isner 7-5, 3-6, 6-3 and Murray advanced after Spaniard Nicolas Almagro retired hurt with what appeared to be a foot injury when trailing 6-2, 1-0. Twice champion Nadal, who beat Murray in last year's final, broke the six-foot-nine Isner in the fourth game of the final set before sealing victory with a forehand winner down the line.
The Spanish left-hander leaned backwards in delight to celebrate his advance to the last eight where he will play Czech Tomas Berdych, who crushed Serbia's Viktor Troicki 6-1, 6-3. "I am feeling really well and I am feeling good on court," said Nadal, who has shaken off the knee injury that forced him to abandon his Australian Open title defence in January this year.
Seventh-seeded American Andy Roddick needed just one break of serve to beat Austrian Juergen Melzer 7-6, 6-4 in a tight match and will next meet Spaniard Tommy Robredo, who battled past Baghdatis 7-5, 0-6, 6-4.
Sixth seeded Swede Robin Soderling brushed aside Frenchman Jo-Wilfried Tsonga 6-3, 6-4 and will face Murray in the last eight. In the women’s section, Fifth seed Agnieszka Radwanska breezed into her second semifinal of the year with a 6-4, 6-3 victory over fourth-seeded Russian Elena Dementieva on Wednesday.
Poland's Radwanska, who also reached the last four in Dubai last month and has yet to drop a set at Indian Wells, broke her opponent twice in each set to win the match in one hour 31 minutes.
The 21-year-old sealed victory when Dementieva hit a backhand service return long and will next meet her good friend and second seed Caroline Wozniacki of Denmark, who overcame a second set hiccup to beat Zheng Jie of China 6-4, 4-6, 6-1.
Reuters