The Spaniard used 29 tyres during the rally, one more than the rules permitted.
He was given a two-minute penalty on Sunday evening, but with the large gaps that had opened up on the attritional rally it only dropped him one place to fourth.
Mads Ostberg therefore picks up a second consecutive third place for M-Sport, strengthening his second position in the championship.
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Hyundai team manager Alain Penasse explained that "an obvious communication error" meant Sordo fitted three new tyres and two used ones in the tyre zone after the long Guanajuato stage on Sunday morning when the quantities should have been the other way around.
"We will now go back to Alzenau and investigate the issue further," said Penasse.
"For sure, this doesn't take away the performance of both the crew and the team throughout this challenging rally."
The original result had meant Hyundai had taken a podium finish in all three rallies since its new i20 made its debut - one for each of its three drivers Sordo, Thierry Neuville and Hayden Paddon.
Sordo had established himself in third early in the weekend and ended up under little pressure in the closing stages after Andreas Mikkelsen crashed his Volkswagen while giving chase on Saturday.
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