Alberto Contador inherited the yellow jersey from Michael Rasmussen at the end of stage 17 of the Tour de France.
Contador will face a challenge from Cadel Evans in Saturday's time trial
Italian Daniele Bennati, part of a breakaway that included David Millar, recorded his first Tour victory with an easy sprint win in Castelsarrasin.
The break finished over nine minutes ahead of Contador, but the Discovery team controlled the peloton, ensuring the Spaniard took the overall lead.
Contador's main rival, Cadel Evans, remains just under two minutes behind.
In a podium ceremony marked by muted applause from the crowd after the day's race, Contador admitted that his overall lead is not ideal.
"I am happy. I feel good, there are three days remaining. I would have preferred to take the yellow jersey in yesterday's stage but there are particular circumstances."
The new leader, who was cleared by a Spanish judge of any involvement in the 'Operation Puerto' doping affair, was adamant that he was clean.
"If I wasn't clean, then I wouldn't be here," he said. "I've undergone all the required doping tests, both at the race and before it.
"Operation Puerto was something which concerned my former team, and I was simply in the wrong place at the wrong time."
Following Rasmussen's exit on Wednesday evening, the stage began without a rider in the yellow jersey.
And, when eight men who were no threat to the overall lead broke clear just 8km from the start, they were allowed to escape.
Bennati and Millar were joined by Martin Elmiger, Daniele Righi, Markus Fothen, Manuel Quinziato, Matteo Tosatto and Jens Voigt but, matched by a high pace in the peloton, the group initially failed to stretch their lead beyond two minutes.
However, by the time the main field reached the feed station after 86km in the baking heat on the comparatively flat 188.5km stage from Pau to Castelsarrasin, there appeared to be an acceptance that the break would be allowed to succeed.
Before the start of the stage, many of the riders had been very clear that they were happy to see Rasmussen go, but the sombre mood of resignation among the Dane's former Rabobank team was palpable.
Having worked tirelessly to secure and protect the yellow jersey, many of the team struggled to find the will to carry on, and it all became too much for Denis Menchov who simply stopped riding and got into the team car near the half-way mark.
From then on, the gap grew to over eight minutes as the breakaway approached the final climb of the day, 19km from the finish.
Plastered in sun-block to protect his skin allergy, Millar was the first to attack, but could not shake off the attentions of the others.
Attacks came and went until Voigt - followed by Bonnati, Fothen and Elmiger - was able to get clear, leaving Millar, Tosatto, Righi and Quinziato in their wake.
The leading quartet weaved around the road playing cat and mouse as they each sought to gain an advantage on each other.
And when Fothen decided to try his luck in the final 500m, Bennati leapt into his slipstream before using his sprinting prowess to power away from the young German.
After his maiden win, the Italian echoed the views of many other riders on the day: "We have to fight against doping," he said.
"I hope the sport will see the end of the tunnel because I think there are riders who do their job honestly."
Stage 17 result:Pau to Castelsarrasin (188.5km)
1. Daniele Bennati (Ita) Lampre, 4 hrs, 14 mins 4 secs
2. Markus Fothen (Ger) Gerolsteiner, @ same time
3. Martin Elmiger (Swi) AG2R, same time
4. Jens Voigt (Ger) CSC, same time
5. David Millar (GB) Saunier Duval, @ 2 mins 41secs
6. Matteo Tosatto (Ita) Quick-Step, @ 2 mins 43 secs
7. Manuel Quinziato (Ita) Liquigas, @ 3 mins 20 secs
8. Daniele Righi (Ita) Lampre, same time
9. Tom Boonen (Bel) Quick-Step, @ 9 mins 37 secs
10. Sebastien Chavanel (Fra) Francaise des Jeux, same time.
40. Geraint Thomas (GB) Barloworld, @ 9 mins 39 secs
110. Charlie Wegelius (GB) Liquigas, @ 9 mins 39 secs
1. Alberto Contador (Spa) Discovery Channel, 80 hrs 42 mins 8 secs
2. Cadel Evans (Aus) Predictor - Lotto, @ 1 min 53 secs
3. Levi Leipheimer (US) Discovery Channel, @ 2 mins 49 secs
4. Carlos Sastre (Spa) CSC, @ 6 mins 2 secs
5. Haimar Zubeldia (Spa) Euskaltel, @ 6 mins 29 secs
6. Alejandro Valverde (Spa) Caisse d'Epargne, @ 10 mins 18 secs
7. Kim Kirchen (Lux) T-Mobile, @ 11 mins 36 secs
8. Yaroslav Popovych (Ukr) Discovery Channel, @ 12 mins 50 secs
9. Mauricio Soler (Col) Barloworld, @ 13 mins 31 secs
10. Mikel Astarloza (Spa) Euskaltel, @ 13 mins 42 secs
45. Charlie Wegelius (GB) Liquigas, @ 1 hr 41 mins 5 secs
68. David Millar (GB) Saunier Duval, @ 2 hrs 24 mins 12 secs
140. Geraint Thomas (GB) Barloworld, @ 3 hrs 38 mins 57 secs.