The Belgium-based team navigated rainy conditions to finish the 16.9-kilometer team time trial with a time of 19 minutes and 24 seconds, with Cavendish taking the blue jersey for crossing the finish line first.
With a time of 19mins 35secs, Movistar were 11 seconds behind the sprinting team of Cavendish, Tony Martin, Michal Kwiatkowski, Zdenek Stybar and Niki Terpstra.
Cadel Evans, Thor Hushovd and Taylor Phinney were in the BMC Racing team that placed third with a time of 19mins 40secs on a course running from San Vincenzo to Donoratico.
After reaching the Tuscan coast, Cavendish said: "Two words, one name - Tony Martin. He did the majority (of the work) today [Wednesday].
"(It was) the planning they put into it but without putting too much pressure on it...We finished with five but everybody had a part to play.
"There are no real egos here, except maybe me, but it was all about getting eight guys from point A to point B as quickly as possible."
The Manx sprinter will defend his lead against Andre Greipel of Lotto Belisol and 2012 Tour de France green-jersey winner Peter Sagan over Thursday's 232km trek to Indicatore.
Team Sky, meanwhile, were 25 seconds behind the winners but a seventh-placed finish leaves team leader Chris Froome in contention for the general classification.
Froome earned an early advantage over two of his biggest rivals as Team Sky gained four seconds on Alberto Contador's Saxo-Tinkoff and 19 second on Joaquim Rodriguez's Katusha.