The Spanish Express beat Boardman by 5min 27sec and his Swiss rival, Tony Rominger, by two minutes to settle any doubts left after his tour of Italy defeat and Boardman's impertinent victory on the first Tour day in Lille.
The first Briton to wear the yellow jersey for 32 years decsribed the stage as 'the most unpleasant time trial of my life.'
'I was completely spent and I just could not try hard, Boardman said. 'I began the race pretty well smashed and there were two problems. Lack of pure natural endurance which is going to take some time to develop, and then there was the heat.
'I really suffered. I started too quick and if I had gone any faster I was going to pass out.'
Indurain, who averaged 50.5kph, looked like a comic- book superhero in his time- trial garb of helmet and goggles as he stormed over the melting roads from Perigueux. Before he had completed the first 7km the yellow jersey was his.
The overnight leader, Johan Museeuw, last to start of the 175 riders, had not even mounted his bike. But that was academic given Indurain's searing show and the Belgian's lack of time-trial speed.
Boardman and the hi-tech Lotus bike, a combination worth Olympic gold and Tour fame, were on a hiding, but so too was everyone else.
By 16km Indurain had overhauled the American, Lance Armstrong. The world road race champion had started two minutes before Indurain. Then with 10km remaining the shadow of Indurain fell on Armand de las Cuevas, who left Perigueux four minutes before the Spaniard. The Frenchman, who skidded on molten tar, finished third fastest.
Rominger had started the doubting about Indurain's infallibility by beating him in the last time trial of the 1993 Tour. Yesterday the Swiss had the panic of a puncture which took 30 seconds to fix, but he still caught the Frenchman, Thomas Davy, who had a two-minute start on him from Perigueux.
Despite his defeat Boardman still rose to seventh overall, 6min 6sec in arrears, and Sean Yates is eighth, 6min 30sec behind.
Even Indurain found the conditions tough, but was content with a 2min 28sec overall advantage over Rominger. 'It would be good to go into the mountains without any stress or nervousness,' he said. 'It was bad on the road because of the heat and the wheels kept sticking in the melting tar which made it difficult.'
Rominger bowed to the superiority of Indurain. 'I felt good and I gave it all I had, but Miguel is just stronger than I am and all I can do is accept it,' said Rominger, whose only remaining choice is to attack in the high climbs and pray for Indurain to have a moment of weakness.
'I'm probably a bit stronger than he is in the mountains and we'll see what happens there, but he looks very good and it will be tough,' he said.
Boardman's focus is now on the world track championships which start in Palermo three weeks after the Tour ends on July 24.
He and his team manager, Roger Le Geay, were busy discussing what to do in the next few days.
'I don't want a complete hiding with the world championships coming up,' Boardman said. 'I don't want to 'kill' myself just to say that I finished the Tour.
'Hopefully I can do a better job next year for the British people who have supported me. Anyway it's not so disappointing for a first Tour.'
TOUR DE FRANCE Ninth stage (64km individual time trial, Perigueux to Bergerac): 1 M Indurain (Sp) Banesto 1hr 15min 58sec; 2 T Rominger (Swit) Mapei Clas +2min; 3 A de las Cuevas (Fr) Castorama +4:22; 4 T Marie (Fr) Castorama +4:45; 5 C Boardman (GB) GAN +5:27; 6 B Riis (Den) Gewiss-Ballan +5:33; 7 T Davy (Fr) Castorama +5:35; 8 A Olano (Sp) Mapei Clas +5:45; 9 A Kasputis (Lith) Chazal +6:01; 10 P Ugrumov (Rus) Gewiss-Ballan +6:04; 11 G Bortolami (It) Mapei Clas +6:12; 12 N Emonds (Bel) Mapei Clas +6:16; 13 L Armstrong (US) Motorola +6:23; 14 J-F Bernard (Fr) Banesto +6:44; 15 S Yates (GB) Motorola +6:50; 16 D Abdoujaparov (Uzbek) Polti +6:52; 17 F Vanzella (It) GB-MG +7:15; 18 J Museeuw (Bel) GB-MG +7:16; 19 V Poulnikov (Rus) Carrera +7:20; 20 V Ekimov (Rus) WordPerfect +7:22. Selected: 25 C Chiappucci (It) Carrera +8:04; 64 G Bugno (It) Polti +10:37.
Leading overall standings: 1 Indurain 41hr 9min 13sec; 2 Rominger +2min 28sec; 3 De Las Cuevas +4:45; 4 Bartolami +5:47; 5 Marie +5:51; 6 Davy +6:04; 7 Boardman +6:06; 8 Yates +6:30; 9 A Olano (Sp) Mapei Clas +6:31; 10 Armstrong +6:35; 11 B Riis (Den) Gewiss-Ballan +6:40; 12 Abdoujaparov +6:45; 13 Museeuw +6:46; 14 Vanzella +6:59; 15 Ugrumov +7:08; 16 L Leblanc (Fr) Festina +8:37; 17 A Peron (It) Polti +9:10, 18 Ekimov +9:21; 19 Poulnikov +9:40; 20 E Zaina (It) Gewiss-Ballan +9:41. Selected: 22 Chiappucci +10:00; 51 Bugno +13:50.
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