Mark Cavendish of Britain won Wednesday's stage and Germany's Stefan Schumacher kept the yellow jersey.
"He was a bit shaken, but he is fine now. He will recover tonight and go again," said Eusebio Unzue, Valverde's sporting director at Caisse d'Epargne. "Nothing serious. He will see the team doctor to have some checks."
Despite the fall, Valverde did not lose any time to Cadel Evans, Carlos Sastre or Denis Menchov ahead of the Tour's first venture into the mountains on Thursday.
It could have been worse.
Last year, pre-race favorite Alexandre Vinokourov had to have stitches in both knees following an early crash. Valverde had much better luck.
"He fell at 55 kilometers (34 miles) per hour," Unzue said. "When you hit the gravel at that speed it is tough. He did not see (the debris), and was surprised."
The 23-year-old Cavendish clinched his first Tour stage win ahead of Spain's Oscar Freire and veteran Erik Zabel of Germany, completing the 144-mile route from Cholet to Chateauroux in 5 hours, 27 minutes, 52 seconds.
"It's the biggest thing that's happened to me," Cavendish said. "To win a stage of the Tour is a massive thing."
Cavendish was selected by British Cycling on Tuesday to ride the madison on the track at the Beijing Olympics along with Bradley Wiggins. The pair won the world championships in the event in March.
"This kid's probably the fastest thing that has come along in the last 15 years," said Cavendish's Team Columbia sporting director Allan Peiper.
George Hincapie, who helped Lance Armstrong win seven consecutive Tours, was equally impressed.
"Cav is such a great cyclist," Hincapie said. "It was really close, but it worked out."
Schumacher held onto his 12-second overall lead over Kim Kirchen of Luxembourg and David Millar of Britain.
Evans is 21 seconds behind in fourth place, and Valverde is 1 minute, 6 seconds behind the Australian in 17th.
Valverde fell about 50 miles into the Tour's longest and flattest stage, while another accident had French cyclist Aurelien Passeron hit a female spectator about 3 miles from the end of the stage.
The spectator, Marie-Antoinette Bidault, a local resident, was helped to her feet quickly by those next to her. Medical staff were soon on the scene and gave her an X-ray, which revealed an injury to her right wrist but no break.
Colombian rider Juan Mauricio Soler, who has ridden with injured wrists since crashing in Saturday's first stage, pulled out of the Tour early in the stage. He was the King of the Mountains champion as the Tour's best climber last year, but a fracture in his right hand made it impossible to defend his jersey.
In Thursday's sixth stage, the riders enter the mountains for the first time, in a 121.5-mile trek through the medium peaks of the Massif Central from Aigurande to Super-Besse. There are two testing climbs - ranked at category 2 - and an uphill finish that could end Schumacher's days in yellow.
Schumacher is not a reputed climber and this could tempt Kirchen, an outsider for overall victory, to attack.
Seventh at last year's Tour - where he finished 41 seconds behind Valverde - Kirchen is looking to become the first Luxembourg rider since Charly Gaul in 1958 to win the showcase race.
"I have never seen Kirchen this strong before," said Marc Sergeant, Evans' manager at Silence-Lotto. "Kirchen has shown he is very good. I was surprised by him, and let's not forget that he was seventh last year."
It may be better news for Evans and Valverde if Kirchen does not take the yellow jersey.
If Schumacher holds the lead for a few more days, then his Gerolsteiner team has to work to protect the jersey. But if Kirchen takes yellow, Evans or Valverde will instruct their teammates to chase him down so that his lead does not get too big - and they would use up vital energy ahead of the bigger mountain stages in the Pyrenees and the Alps.
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Associated Press Writer Naomi Koppel contributed to this report.