Santiago Botero won Wednesday's time-trial stage of the Dauphine Libere, with Lance Armstrong third.
Botero beat Armstrong by more than 25 seconds
The Colombian edged out American Levi Leipheimer, who took the overall lead, by one second with the six-times Tour de France champion 26secs adrift.
Botero completed the 46.5km stage in one hour six seconds.
Armstrong said: "I'm not overwhelmingly pleased but I'm not disappointed. It was hard - 100% effort all the way. I'm on my schedule (for the Tour)."
Armstrong had said the stage was an important stepping stone in his preparation for the Tour next month.
The director of Armstrong's Discovery Channel team, Johan Bruyneel, said: "We needed a real test, and in this sense it is a good performance.
"This time trial was really the stage that mattered, the real test for us. And from what I saw, we have every reason to be satisfied."
"There's still some work ahead of us but the timing is right," said Bruyneel, adding that Armstrong's performance in the rest of the Dauphine Libere depends on "his sensations".
Armstrong, who has yet to win a race this season, said he felt Leipheime was now the favourite for overall victory in the Dauphine Libere.
Thursday's fourth stage takes the riders over 182 km up the gruelling Mont Ventoux, a climb the American has never won.
However, winning a seventh Tour de France in July is the only thing that really matters for Armstrong and Leipheimer said the Tour was also his main goal this season.
"I didn't know what to expect in this time trial. I thought Botero, Lance and Landis were the favourites," said Leipheimer.
"But I had done a good prologue and I have been using a new bike here in the Dauphine which suits me fine.
"Of course, if I have a chance for the overall classification I will not let it pass, but my main objective is the Tour.
Botero, winner of his second Dauphine Libere time trial after his 2002 victory, also has a good chance of overall success.
Stage three result:
1 Santiago Botero (Col) 1hr 00min 06sec
2 Levi Leipheimer (USA) +1sec
3 Lance Armstrong (USA) +26
4 Floyd Landis (USA) +39
5 Alexandre Vinokourov (Kaz) +1min
6 Oscar Pereiro (Spa) +1:09
7 George Hincapie (USA) +1:11
8 Marzio Bruseghin (Ita) +1:14
9 Jose Ivan Gutierrez (Spa) +1:16
10 Sebastian Lang (Ger) +1:19
1 Levi Leipheimer (USA) 11hrs 11mins 20secs
2 Santiago Botero (Col) +12secs
3 Lance Armstrong (USA) +30
4 Floyd Landis (USA) +42
5 George Hincapie (USA) +1min 09secs
6 Alexandre Vinokourov (Kaz) +1:12
7 Oscar Pereiro (Spa) +1:14
8 Jose Ivan Gutierrez (Spa) +1:27
9 Marzio Bruseghin (Ita) +1:36
10 Sebastian Lang (Ger) +1:43