The Swedish time trial champion from the Vacansoleil-DCM team posted a time of 11 minutes and 19 seconds on the 9.4km course outside Paris.
That was marginally better than Team Sky's Wiggins who went off the start ramp third from last in wet conditions.
Omega Pharma-Quick Step's Levi Leipheimer was third, a further three seconds adrift, ahead of fellow American Tejay van Garderen (11:22) and Thomas De Gendt (11:25).
"We made the right choice by starting in the middle of the field. It was much better than for the guys at the end," Larsson said.
"I wasn't really sure of myself because it was only my second race this season. My legs were very hard but, as good as they were, it did it."
Asked he if could win the race, Larsson, the tallest rider in the peloton at 1.94 metres, was not optimistic.
"We will see, it's very hard when you get to the big mountains but we will try to hang on to it as long as possible," he said.
Defending champion and world time trial champion Tony Martin started last in the rain and finished 23 seconds behind the winner in 28th.
Spaniard Alejandro Valverde, back this season after a doping ban and one of the pre-race favourites, finished a disappointing 41st, 30 seconds off the pace.
The "Race to the Sun" ends in Nice next Sunday.