Etixx-QuickStep, who won their third title since the event was created in 2012, clocked 42min 32.39sec on a 40km pan-flat course in searing heat, beating BMC by 11.69sec.
Tony Martin and fellow German Marcel Kittel, Belgians Julien Vermote and Yves Lampaert, Dutchman Niki Terpstra and Luxemburg's Bob Jungels produced a flawless ride on a technical course, finishing strongly.
Australia's Orica-Bike Exchange took third place, 37.12 off the pace.
“We rode as a team and fought against ourselves, riding to the limit, and it wasn’t easy, as the heat made things complicated," Martin said. "It’s very special to win my last race with Etixx-QuickStep.
"I’ve raced all the team time trials since the discipline returned at the Worlds, came every time on the podium and won twice, but this victory is different. I want to thank the team for today and for these five years, they were incredible.”
Etixx-QuickStep made the fastest start, clocking 15:11sec at the first intermediate checkpoint, two seconds ahead of BMC.
The American team, winners of the last two editions, were only seven-hundredths of a second behind at the second checkpoint but could not sustain the pace.
"We did everything we could leading up to it and you can't win them all," Australian Rohan Dennis said. "I think we rode just as well as last year but Etixx-QuickStep were just better on the day so hats off to them.
"The first 30km felt ok but it was the last 10km that really hurt, especially with the change of pace with the corners. Obviously the heat played a part, I think that was the main factor, and it was quite smooth until we came into The Pearl.
"Of course it makes us hungrier for next year but a year is a long time and I've got the individual time trial on Wednesday to focus on."
Team Sky, third at the first checkpoint, dropped to fourth at the second and were eventually beaten by Orica-Bike Exchange for third place.
Boels Dolemans, who also include reigning road race world champion Elizabeth Deignan (formerly Armistead) and four-time world champion Ellen van Dijk, blew away the opposition to finish the 40km course in 48mins 41.62secs.
Almost a minute ahead of their nearest rivals, Germans Canyon Sram Racing, who finished in 49:29.86.
Twenty16-Ridebiker, the first team out on the course, which started in Lusail where the 2022 football World Cup final will be played, finished third.
“We’ve worked hard all season,” Deignan said. “We’ve shown ourselves to be the most dominant team in women’s cycling, and it was really important to us to finish off the season with this medal. It’s been a long season, and I’m so proud of how the team came together."