The nine-man team, which includes Sir Bradley Wiggins, finished the 17.4 kilometre course nine seconds ahead of second-placed Movistar, with Astana a further five seconds back.
The result means Sky Procycling’s Salvatore Puccio will wear the leader’s pink jersey today based on yesterday’s classifications, with Wiggins second and team-mate Sergio Henao completing the overall top three with the same time.
Mark Cavendish will wear the red jersey for overall points leader on the 222km route to Marina Di Ascea after his Omega Pharma Quick-Step team finished in 17th place.
Team Sky took the plaudits on the second day after they crossed the line with five riders in a time of 22 minutes and five seconds.
For Puccio, a 23-year-old Italian debutant, being presented with the race leader’s maglia rosa jersey was a proud moment.
“Today was an incredible result and it is a huge surprise. I could never have thought this morning that I would be pulling on the maglia rosa. It is incredible,” said Puccio.
“Once again the team showed how strong we are. Everyone put in a huge effort and it is very satisfying to be part of a big team result like this. For an Italian rider the maglia rosa is one of the best things that can happen to you.”
Puccio took the jersey from Cavendish, after his team were unable to maintain the 20 second buffer he earned with yesterday’s opening stage win.
BMC Racing, for whom Sheffield’s Adam Blythe, 23, rides, finished 12th in the time trial.
On Saturday, Blythe finished a very creditable seventh behind Cavendish after a big crash wiped out a number of challengers.
Blythe said: “I was a bit blocked when the sprint started, which was a bit of a shame because Taylor Phinney did an amazing job for me. Hopefully, I’ll get another chance like that and we can have another go of it. I haven’t done many bunch sprints in a long time – since the Tour of Qatar almost. So hopefully there are more to come.”
Yorkshire time-trial ace Joel Wainman notched up another big win on Saturday, taking victory in the Yorkshire Cycling Federation 25-mile event in North Yorkshire by a comfortable margin.
Wainman, 38, from Hessle, clocked 52min 1sec for the V236 course which takes the riders from Topcliffe to South Kilvington and back twice. That time was good enough to give him the win by 2-19 over his colleague at Team Swift, 43-year-old Simon Beldon from Adel, while third spot went to Ged Millward, the 48-year-old Ilkley CC rider. Best of the women was Harrogate Nova’s Joanne Ketteringham with 1-04-35.
Time-triallers from across the region will be in action in the Yorkshire CF 10 at Boroughbridge tomorrow.