World champion Muller lead from pole position and remained in front for the duration of the first race, with Tiago Monteiro keeping Huff at bay to take second ahead of the Briton who crossed the line in third.
Norbert Michelisz came fourth ahead of bamboo-engineering duo of Alex MacDowall and James Nash.
Race two contained much more drama, as two huge pile-ups and red flags saw the field ripped apart, with Huff eventually prevailing following the two restarts from behind the safety car.
Tom Coronel had lead for most of the race from pole, but the stop-start nature of the race handed the initiative to the faster SEAT and Chevrolet cars, with Huff finally claiming the lead with two laps remaining.
Pepe Oriola also outstripped Coronel to claim second, pushing the Dutchman into third.
Nash finished in fourth ahead of team-mate MacDowall, to the the pair a one-two finish in the Yokohama Trophy.
Huff was delighted to finish the season strongly
"What an amazing race. I started P7 and in the end I overtook 12 people and finished P1," he told www.fiawtcc.com.
"Just amazing. So happy for the boys. Double podium this weekend - what a way to finish."