Spain's Oscar Freire (Rabobank) won Thursday's fifth stage from Beauvais to Caen, taking an alternative route down the right, while the other sprinters went up the left.
Freire surprised the other sprinters, got a gap and used his power to stay clear to the line. Boonen went across the road to try and match Freire but could only follow him across the line for second place. Inaki Isasi (Euskaltel) was third, with Robbie McEwen (Davitamon) only fifth after getting stuck behind Boonen.
David Millar (Saunier Duval) finished 31st in the main bunch, while Bradley Wiggins (Cofidis) sat up in the final kilometres after working for Jimmy Casper and finished 153rd at 2-14.
"Every sprint at the Tour is difficult and they?re always dangerous. I had good position today which is important. I started well back but it worked," Freire said.
"I?ve won two Tour stages (his other was in 2002) and I'd like to win at least another stage but the green jersey is a bit difficult because you need a good team and Rabobank also have to look after Rasmussen and Menchov.?
Thanks to the 20, 12 and 8 second time bonuses awarded to the first three on the stage, Boonen extended his lead on Michael Rogers (T-Mobile) to 13 seconds. Freire moved up to third at 17 seconds.
?I?m disappointed for the team more than myself,? Boonen said after missing out on the stage win again.
"I?m satisfied because I?m still in yellow and I?ve got some points back in the points competition but the reason I lost the sprint was that I was too eager to win. I went early on the left and it was windy and then I got tangled up with some other riders.?
"The Tour sprints are al about circumstances. Two years ago I was getting my ass kicked in the first week and then I won on the Champs Elysees. Sometimes you win and sometimes you lose but you?ve got to stay positive. I?ve still got the yellow jersey.?
The early heroes of the day were Samuel Dumoulin (AG2R-Prevoyance) and Bjorn Schroder (Milram). They were part of an eight-rider move that formed after 25km and then went clear in tandem after 37km. They opened a maximum lead of 12-50 but were gradually pulled back thanks to Quick Step and Davitamon and were caught four kilometres from the finish.
1 Oscar Freire (Spa) Rabobank 225km in 5.18.50 (42.341 km/h)
2 Tom Boonen (Bel) Quick-Step-Innergetic
3 Inaki Isasi (Spa) Euskaltel-Euskadi
4 David Kopp (Ger) Gerolsteiner
5 Robbie McEwen (Aus) Davitamon-Lotto
6 Alessandro Ballan (Ita) Lampre-Fondital
7 Thor Hushovd (Nor) Crédit Agricole
8 Francisco Ventoso (Spa) Saunier Duval
9 Erik Zabel (Ger) Milram
10 Bernhard Eisel (Aut) Francaise Des Jeux
Overall standings after stage 5
1 Tom Boonen (Bel) Quick-Step-Innergetic 25.10.51
2 Michael Rogers (Aus) T-Mobile 0.13
3 Oscar Freire (Spa) Rabobank 0.17
4 George Hincapie (USA) Discovery Channel
5 Thor Hushovd (Nor) Crédit Agricole 0.19
6 Robbie McEwen (Aus) Davitamon-Lotto 0.24
7 Paolo Savoldelli (Ita) Discovery Channel 0.27
8 Floyd Landis (USA) Phonak 0.28
9 Vladimir Karpets (Rus) Caisse d'Epargne-Illes Balears 0.29
10 Serguei Gonchar (Ukr) T-Mobile same time.
Thank you for reading 20 articles this month* Join now for unlimited access
Enjoy your first month for just £1 / $1 / €1
*Read 5 free articles per month without a subscription
Join now for unlimited access
Try first month for just £1 / $1 / €1