Kopecký, in a factory ŠKODA Fabia Super 2000, had trailed Mikkelsen's ŠKODA UK entry by 3.6s starting the final 16.12-kilometre test. But with Mikkelsen losing vital speed he was powerless to defend his advantage as Kopecký raced to his first win of the Intercontinental Rally Challenge season and his second on Gran Canaria following his maiden triumph in 2010.
Mikkelsen had to settle for the runner-up spot, 28.3s behind Kopecký but extends his lead in the IRC drivers' standings, while ŠKODA, now unbeaten on this event for the three years, claims maximum IRC manufacturers' points for the second time this season.
"I heard he had some problems with the engine, which is a pity because it was a nice battle the whole weekend," said Kopecký. "Winning because of his problem does not make me so I happy but thanks to ŠKODA and my co-driver who today did a really great job."
A dejected Mikkelsen, who led after all but two stages of the 15-stage rally, said: "I had no engine power, it was misfiring all the way. There was no power at all and it's very disappointing because I was so close to my first win on Tarmac. It's a shame. We felt it at the end of the second last one but there is nothing we could do."
Luis Monzón was the top Peugeot finisher and the leading Spaniard in an impressive third overall with Sepp Wiegand a fine fourth on his Canarias debut for ŠKODA Auto Deutschland.
Jonathan Perez took fifth in another Peugeot with Joan Vinyes winning the IRC 2WD Cup in sixth position.
Robert Consani bagged IRC Production Cup honours for Renault in 12th overall but there was late agony for Briton Harry Hunt who dropped out of the top 10 to 13th when his car's engine cut out two kilometres from the finish of the final stage.
Final results from Rally Islas Canarias El Corte Inglés can be found here.