The Spaniard managed to hold off the fast-starting BMW of Dirk Muller at the start, with the pair banging wheels on the run down to the first corner.
Muller's car was briefly launched up onto two wheels and the German's loss of momentum managed to allow Gene's teammate Peter Terting to retake second place - which proved crucial for the rest of the race.
As Gene set about building up a lead, Terting managed to hold up the much quicker Muller for several laps before finally yielding second place on lap five.
By that stage, however, Gene was too far ahead to be captured and he eventually took the chequered flag 3.2 seconds ahead.
"Tonight I am not going to sleep because the emotion I have at the moment is unbelievable," said Gene. "To come to Spain and have this result is just amazing."
Behind Muller, Terting held onto third place to make it two SEATs on the podium, with Andy Priaulx eventually managing to salvage fourth place after starting down in 15th.
Priaulx had stayed out of trouble on an incident-filled first lap to initially move up to sixth, before getting past Gabriele Tarquini on lap five and then Fabrizio Giovanardi on lap nine.
The result leaves Dirk Muller with a two-point lead over Priaulx in the title chase, with Giovanardi a further six points adrift.
Alex Zanardi will start this afternoon's second race from pole position after taking eighth place in race one.
CLASSIFIED: Pos Driver Car Time 1. Jordi Gene SEAT Leon 22:48.757 2. Dirk Muller BMW 320i + 3.288 3. Peter Terting SEAT Leon + 7.099 4. Andy Priaulx BMW 320i + 8.417 5. Jorg Muller BMW 320i + 10.928 6. Fabrizio Giovanardi Alfa Romeo 156 + 15.506 7. Nicola Larini Chevrolet Lacetti + 19.414 8. Alessandro Zanardi BMW 320i + 19.937 9. Stephane Ortelli SEAT Toledo Cupra + 25.285 10. Marc Carol SEAT Toledo Cupra + 26.214 11. Adriano De Micheli Honda Accord Euro R + 28.953 12. Giuseppe Ciro BMW 320i + 31.876 13. Tomas Engstrom Honda Accord Euro R + 32.654 14. Antonio Garcia BMW 320i + 42.743 15. Polo Villaamil SEAT Toledo Cupra + 45.121 16. Gabriele Tarquini Alfa Romeo 156 + 53.181 17. Stefano D'aste BMW 320i + 1 Lap NOT CLASSIFIED/RETIREMENTS: Driver Car On Lap Augusto Farfus Jr. Alfa Romeo 156 9 Tom Coronel SEAT Toledo Cupra 9 Rickard Rydell SEAT Leon 6 Carl Rosenblad BMW 320i 4 Alain Menu Chevrolet Lacetti 4 James Thompson Alfa Romeo 156 2 Thomas Klenke Ford Focus 2 Michael Funke Ford Focus 2 Marc Hennerici BMW 320i 2 Robert Huff Chevrolet Lacetti 1 Fastest Lap: Dirk Muller, 1:43.795 on lap 3
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