The 33-year-old finished 46 seconds behind defending champion Tony Martin, who captured his third title in a row in Tuscany.
Wiggins said that his end-of-season form, which saw him victorious in the recent Tour of Britain, sets him up perfectly for next year.
"There is always a tinge of disappointment because you can't be world champ but in the same time you have to accept when you are beaten by a better athlete on the day," the 2012 Tour de France champion told reporters.
"I'm pretty happy. It's been a long summer but quite a successful one with the win in Poland, the Tour of Britain and this.
"It's a great platform to go through the winter and to next year."
Switzerland's Fabian Cancellara was beaten into third place by two seconds.