The former Intercontinental Rally Challenge champion was 10.8s faster than SKODA Motorsport team-mate Jan Kopecky on the 23.38-kilometre Maják stage.
"It was good," said Hanninen, winner of a record 10 IRC rallies and champion in 2010.
"I really was pushing - that I can promise. We are here and that’s nice."
Kopecky stands second, 1:15 ahead of Roman Kresta who benefited from Tomas Kostka’s "big moment" on the stage to go third in his self-funded Fabia.
Kostka completed the stage with a damaged wheel rim and now trails Kresta by 8.6s.
Andreas Mikkelsen had to be cautious, finishing fifth on the stage after using both of his spare tyres on stage 10 because of punctures. He has fallen from being a contender for top spot to ninth overall, 5:34 off the pace.
The fight between Hanninen and Kopecky had intensified on the rain-hit stage 11, the 11.42km Kudlovice run.
Hanninen kept his lead after going just 0.2s faster despite cracking his windscreen on a branch.
"I am on the hardest [compound] tyre from the stock so it’s quite interesting,” said the Finn.
Kopecky said: “It’s really crazy weather. The forecast is not for rain but it’s raining like hell on this stage and 15 kilometres away it’s full sunshine.”
After the opening stage of the day, stage 10, saw defending champion Mikkelsen stopping twice with punctures, he said: "It was going into a junction, I just took some extra space, went over a kerb and it must have been big enough to get a puncture on both wheels.
"I thought I would be okay but we needed to stop two times because of this. I changed one but then had to stop again. It was not a good stage."
Mikkelsen was thankful that he was the only driver among the leading trio to carry two spares: one a medium-compound slick tyre with a 'w' cut to cope with the damp conditions in the forest areas and the other a soft, again with a ‘w’ cut at the rear.
Hanninen suffered a spin early on the stage on hard-compound slicks, which ultimately saw him lose 6.2s to stage winner Kopecky who closed the gap to 5.2s.
"It was very tricky because it was raining quite a lot from the middle of the stage,” said the Czech, who ran mediums. "There was fog and it was dark and you were not able to see the road."