Contador powered his way to victory in picturesque Annecy
Bradley Wiggins gave himself a good chance of a podium finish at the Tour de France after making ground on his rivals in Thursday's time trial.
The British Garmin rider moved from sixth to fourth spot overall, just 11 seconds behind Lance Armstrong, who moved up one place to third.
Champion-in-waiting Alberto Contador was fastest over the 40.5km course, finishing in 48 minutes 30.72 seconds.
Saxobank rider Andy Schleck lies second overall, just over four minutes adrift.
Friday's largely flat stage is likely to have little impact on the final placings but the 20th stage on Saturday, 167km (103.8 miles) from Montelimar to Mont Ventoux, is likely to decide who takes the other two podium spots on Sunday behind Contador.
The Spaniard produced a remarkable performance on Thursday and he is now set to win his second Tour, having previously triumphed in 2007.
Having proved he is the master of the mountains he showed he is also one of the best time triallists, but insisted his only intention had been to cement his position in the general classification (GC).
"For me to win a time trial at the Tour, it's just huge," said the Astana ace.
"I went out hard but thinking only to protect my place in the GC. But when I got to the first time check and saw my time it gave me a bit more belief.
"After that I just went as hard as I could to the finish. It was a crucial day for me, and I came through it far better than I expected."
Contador finished three seconds ahead of Olympic champion Fabian Cancellara and one minute 45 seconds ahead of nearest rival Andy Schleck.
Schleck's brother and fellow Saxobank rider Frank dropped from third overall down to sixth while Astana's Andreas Kloeden remains in fifth, two seconds behind Wiggins.
Wiggins, a three-time Olympic track cycling champion, will find it difficult to close the gap on Armstrong, who will have the might of his Astana team-mates to help him during Saturday's slog up Mont Ventoux.
Nevertheless, the 29-year-old has impressed in the mountains and will look to his Garmin team-mate Christian Vande Velde to help him stay in touch with his rivals.
Time-trial dangerman Wiggins was looking to eat into the advantage his rivals had over him, and midway through the Annecy route it appeared that the Londoner was set to post a fast time, but in the final few kilometres the Briton faded to finish 43 seconds behind Contador.
Compatriot and time-trial specialist David Millar came home fifth on a course he believed favoured the climbers because of the category three climb over the Bluffy pass, which wound upwards for 3.7km (2.3 miles) three-quarters of the way through the stage.
"I felt like I had stopped dead in my tracks, on the climb," he said.
Stage 18 result:
1. Alberto Contador (Spain / Astana ) 48mins 30secs 2. Fabian Cancellara (Switzerland / Saxo Bank ) +3" 3. Mikhail Ignatiev (Russia / Katusha ) +15" 4. Gustav Larsson (Sweden / Saxo Bank ) +33" 5. David Millar (GB / Garmin ) +41" 6. Bradley Wiggins (GB / Garmin ) +43" 7. Luis Leon Sanchez (Spain / Caisse d'Epargne ) +44" 8. Christophe Moreau (France / Agritubel ) +45" 9. Andreas Kloeden (Germany / Astana ) +54" 10. David Zabriskie (US / Garmin ) +1:02"
120. Charlie Wegelius (GB / Silence-Lotto) 5:18" 127. Mark Cavendish (GB / Team Columbia) 5:29"
1. Alberto Contador (Spain / Astana ) 73hrs 15mins 39s 2. Andy Schleck (Luxembourg / Saxo Bank ) +4:11" 3. Lance Armstrong (US / Astana ) +5:25" 4. Bradley Wiggins (GB / Garmin ) +5:36" 5. Andreas Kloeden (Germany / Astana ) +5:38" 6. Frank Schleck (Luxembourg / Saxo Bank ) +5:59"
14. Carlos Sastre (Spain/Cervelo) +15.26" 61. Charlie Wegelius (GB/Silence-Lotto) + 1:19.43" 71. David Millar (GB/Garmin) + 1:30.38"
141. Mark Cavendish (GB/Columbia) + 2:56.54"
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