Last of the 198 riders to start the eight-kilometre time trial, the shy giant from Villava clocked 9 min, 22 sec, to win by two seconds.
No other riders, including all Indurain's rivals for overall victory, finished within 10 seconds of him.
Until Indurain raced home before screaming fans, new professional Alex Zulle, from Switzerland, held a one second lead over Frenchman Thierry Marie, winner of the last two Tour prologues.
Greg LeMond, chasing a fourth Tour triumph, was 14 seconds slower than Indurain who, three weeks ago, won the Tour of Italy.
Now Indurain is set to try for a rare double of two major tour victories in the same year. This was last achieved by Dubliner Stephen Roche, who yesterday finished 20 seconds off the pace.
Tension heightened yesterday on the Tour after saboteurs destroyed seven vehicles, including three belonging to Channel Four television, at Hondarribia.
The early-morning fire in a hotel car park came hours after two cars, one from French television, were set ablaze in a car park under yesterday's finish area.
Today, the 198 riders race through the Basque countryside passing through Hondarribia on a 194-kilometre leg that starts and finishes in San Sebastian.
Tomorrow, the Tour heads out of the coastal resort, bracing itself for the possibility of more strife as it returns to the French blockades.
TOUR DE FRANCE Prologue (San Sebastian, Sp): 1 M Indurain (Sp) 9min 22sec; 2 A Zuelle (Swit) +2sec; 3 T Marie (Fr) +3; 4 J Nijdam (Neth) +4; 5 A de las Cuevas (Fr) +11; 6 A Garmendia (Sp) +12; 7 R Alcala (Mex); 8 G Bugno (It); 9 E van Hooydonck (Bel) all s/t; 10 V Ekimov (CIS) +13; 11 E Breukink (Neth) +14; 12 F Moreau (Fr); 13 E Vanderaerden (Bel); 14 G Bontempi (It); 15 G LeMond (US) all s/t; 16 A Kasputis (Lith) +16; 17 J Durand (Fr) +18; 18 F Maassen (Neth); 19 R Golz (Ger) both s/t; 20 A Chiurato (It) +20. Selected: 22 Stephen Roche (Irl) +20; 93 S Kelly (Irl) +39; 102 R Millar (GB) +40; 128 S Yates (GB) +47; 183 M Earley (Irl) +1:02.
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