Bradley Wiggins' Vuelta a Espana hopes were hit by a chaotic start, which saw Team Sky finish third-from-last in the opening team time trial in Benidorm.
But Mark Cavendish's team HTC-Highroad were just nine seconds behind winners Leopard Trek in the 13.5km stage.
Key Sky rider Kurt-Asle Arvensen crashed early and the team struggled to recover, finishing 42 seconds back.
But sports Director Steven de Jongh said: "Kurt is looking really fit and Bradley is looking super strong."
He told the team website: "If you look at the overall picture with some of the main contenders Bradley lost some time but to most of them he lost around 20-25 seconds.
"It is a loss of course and we aren't happy with it but it could be worse."
Wiggins was back in action for the first time since crashing out of last month's Tour de France with a broken collarbone.
World time trial champion Fabian Cancellara was vital for Leopard and later tweeted: "This is my biggest surprise victory in my career."
Jakob Fuglsang was first over the line for the team, who took 16 minutes 30 seconds over the course.
He takes the leader's red jersey from defending champion Vincenzo Nibali, whose Liquigaz team were second.
Cavendish should get his first chance of a stage victory on Sunday, at the end of a 174km stage from La Nucia to Playas de Orihuela, with American Tyler Farrar his biggest rival.