The 37-year-old arrives at the British outfit following a stint as head coach for the Australian Olympic team at the London Games in the summer.
Stephens leaves his posts as head coach and programme manager at the Australian Institute of Sport and Triathlon Australia and will now work alongside Sky's head of performance Tim Kerrison.
“I believe it is (Team Sky boss) Dave Brailsford’s vision of introducing a diversity of skill sets into Team Sky, and ultimately the cycling staff and riders’ embracement of new training and competition strategies, that has given Team Sky a competitive advantage over other teams," Stephens said.
“I’m looking forward to contributing to the team and bringing in new ideas through my sport science and coaching knowledge of triathlon."
Brailsford said: “Shaun’s appointment continues Team Sky’s commitment to assembling the very best coaching and support staff in the world, without being afraid to look beyond the arena of cycling.
“It is incredibly exciting to be bringing fresh expertise into the sport, and further reinforces this team’s desire to break new ground in the field of performance.
“The team has taken tremendous strides since the appointment of Tim Kerrison, who came from swimming, and we hope that with Shaun on board we can maintain our position as the world’s number one cycling team.”