Second seed and defending champion Yanina Wickmayer demolished Simona Halep of Romania 6-0 6-2.
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The 20-year-old will face either Marcos Baghdatis or second seed Rafael Nadal in the third round.
Second seed Mikhail Youzhny was also beaten, losing 6-2 6-0 to defending champion Jonas Bjorkman .
Djokovic's defeat means second seed Andy Murray is the highest-ranked player left in the draw.
Second seed Elena Dementieva of Russia plays Angelika Roesch of Germany on Wednesday night.
Second seed Sjeng Schalken followed Novak out, when he was beaten 6-3 6-4 by Thomas Enqvist.
Second seed Nicolas Kiefer pulled out of the event in Halle due to a recurring wrist injury.
Second seed Nadal defeated Gael Monflis in straight sets, to book his place against compatriot Nicolas Almagro.
Second seed Stepanek won 6-2 6-1 against Frenchman Gael Monfils, who was struggling with a shoulder problem.
The second seed now plays another Russian, 2004 champion Mikhail Youzhny, for a place in Sunday's final.
Second seed Amelie Mauresmo of France faces a tough opener against 1994 Wimbledon champion Conchita Martinez of Spain.
Second seed Massu was also seeking his second title of the year, but came up short against Sanchez.
Lisnard will face a tough task in the semi-finals when he plays second seed Paradorn Srichaphan of Thailand.
Henin came from behind to oust second seed Caroline Wozniacki, beating the young Dane 6-7 (5-7) 6-3 6-4.
The second seed triumphed 6-3 6-2 6-4 in just one hour and 55 minutes to reach the semi-finals.
Second seed Guillermo Coria stormed into the third round with a 7-6 6-3 win over France's Paul-Henri Mathieu.
Second seed Zvonareva cruised past Jelena Jankovic 6-3 6-0 in the opening round-robin match in the White Group.
Italian second seed Francesca Schiavone came from a set down to beat Bulgarian Tsvetana Pironkova 3-6 6-3 6-1.
She will meet American Jill Craybas in the final, who upset second seed Tamarine Tanasugarn 6-4 4-6 6-4.
Second seed Roddick found things a bit tougher than Federer, but still won in three sets, 6-3 7-6 7-6.
Second seed Nadal reached the quarterfinals for a sixth successive year after beating 13th-seeded American John Isner 7-5 6-4.
Australian second seed Sam Stosur joined Serena in the third round after defeating American wildcard Jamie Hampton 6-0 7-5.
Kerber battled past the second seed 7-6 5-7 6-3 to land her first career title after a superb week.
Elsewhere, second seed Elena Dementieva fell in three sets to Germany's Angelika Roesch.
Meanwhile at the ATP event in Estoril, second seed Richard Gasquet of France reached the third round in fine style.
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The winner of that match will play either big-serving American second seed John Isner or Swiss No. 4 Stanislas Wawrinka.
World No. 6 Nikolay Davydenko is the second seed, and the Russian's first match is against Feliciano Lopez of Spain.
Second seed Novak Djokovic and defending champion Andy Murray are among the big names to have already departed the event.
In the women's final, Italian top seed Sara Errani breezed past second seed Carla Suarez Navarro of Spain 6-0 6-4.
Davydenko will play second seed Rafael Nadal in the final after the Spaniard earlier made short work of Viktor Troicki.
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