Loeb finished the final Ouninpohja 2 stage 6.1 seconds ahead of Hirvonen, who lost precious time in the morning when he hit a tree. Latvala was a further 28.9 adrift.
Norway's Petter Solberg was fourth in a Ford.
The victory was Loeb's sixth in eight races this season, 73rd of his career, and he led from start to finish. The Frenchman now has 171 points to Hirvonen's 128 with five rounds remaining.
"It's very satisfying to win in Finland," said the Frenchman. "I didn't come here especially to win, I came for points because it's very difficult to beat the Finnish drivers.
"It was a great fight with Mikko, a one-two for Citroen and great for the championship."