American Bookwalter, Taylor Phinney, Michael Schär, Lawrence Warbasse and Greg Van Avermaet completed the 14km Al Rufaa Street course in 16:07.
That was five seconds quicker than Sky's squad of Edvald Boasson Hagen, Bernhard Eisel, Mathew Hayman, Gabriel Rasch, Luke Rowe, Ian Stannard, Chris Sutton and Geraint Thomas.
Bookwalter, who outsprinted two breakaway companions to win stage one in the 12th edition of the race rated as a 2.HC event on the UCI Asia Tour, leads compatriot Phinney by six seconds on GC with Adam Blythe - who like fellow Britain Stephen Cummings lost contact with his BMC team-mates towards the end of the TTT - four seconds further back in third.
Bookwalter said the team did not panic when it reached the halfway point nine seconds slower than Sky.
"My biggest worry was that we would get too excited and blow guys up," he said.
"I felt like we already had a consistent pace and we were actually cautious on the turnarounds. So maybe we lost a couple seconds there. But I was confident the energy we saved was going to come through near the finish. Taylor (Phinney) and Michi (Schär) were ridiculously strong at the end."
BMC fill the top five places on GC followed by Team Sky trio Eisel (+11 seconds), Boasson Hagen (+15) and Welshman Thomas (+15).
The Arabian state’s pan-flat roads will provide a haven for sprinters in the four remaining stages although crosswinds can cause havoc.
Omega Pharma 16:17
Saxo Tinkoff 16:33
AG2R finish 16:40
IAM Cycling 16:44
Champion System 17:22