Manninen, who has three World Cup titles and leads the Nordic combined standings this year, had never previously won an individual gold medal at the Olympics or the world championships.
"This is my dream and my goal," said Manninen. "I've spent so much time thinking of this moment and now I am relieved and happy."
Germany's Bjorn Kircheisen went into the cross-country portion of the event with a 16-second lead after nailing the longest jump of 439.63 feet on the large hill.
Manninen started the cross-country race in ninth place, 49 seconds off the lead after a jump of 125 meters. He finished with a time of 17 minutes, 40.2 seconds.
Norway's Magnus Moan was 0.03 seconds off the pace for silver while Kircheisen took bronze.
"The finish with Magnus was very tough," added Manninen. "I had to do everything I could to win. I knew I was very strong in that kind of finish, I knew I had a chance and that I couldn't miss it."
Japan's Daito Takahashi suffered a horrendous crash when his left ski became elevated during his jump on the large hill.
Takahashi was taken to a nearby hospital and was diagnosed with a broken left shoulder.
In cross-country events, Cristian Zorzi edged Russia's Vassili Rotchev in a photo finish as Italy took the men's team sprint gold medal.
Russia took the lead just before the last changeover, but Zorzi completed a strong final lap to give Italy its first medal of the meet. The Czech Republic finished third.
Tor Arne Hetland crashed out midway through the final and favorite Norway finished a disappointing seventh. Olympic gold medalist Sweden failed to qualify for the final.
The Italian team of Zorzi and Renato Pasini finished with a time of 17 minutes, 50.6 seconds.
In the women's team sprint, World Cup leader Virpi Kuitunen and Liisa Riitta Roponen of Finland captured the gold medal with a winning time of 16:20.9.
The German team of Evi Sachenbacher Stehle and Claudia Kuenzel-Nystad took silver.
Defending champions Norway, comprising individual sprint gold medalist Astrid Jacobsen and defending World Cup sprint champion Marit Bjorgen, finished over three seconds back in third place.
The 2007 championships mark the first time the meet is being held as an independent event in Asia. In 1972, when the Olympic Winter Games were held in Sapporo, they doubled as the FIS World Ski Championships.
The competition will continue Saturday with the cross-country 9.32 miles pursuit and ski jumping events.