Despite the setback, Quick-Step were able to regroup and only lost a further three seconds on BMC heading through the second checkpoint and finished a total of seven behind them in third place.
Among the overall favorites, Dumoulin was seventh (11 seconds behind), last year's runner-up Rigoberto Uran was 10th (:35), Porte was 14th (:51), Movistar teammates Alejandro Valverde and Mikel Landa were 17th (:53), Froome was 18th (:55), Adam Yates was 20th (1:00) and 2014 champion Vincenzo Nibali was 22nd (1:06).
Defending champion Chris Froome made up for some lost time as his Team Sky finished second. "We know that Peter (Sagan) is one of the greatest riders of the peloton and I'm happy to compete against him because he makes everything more hard", he explained. Van Avermaet failed to win a spring Classic and teams are afraid to commit a significant chunk of their budgets beyond 2019.
Chris Froome is barged off the road in controversial fashion as Fernando Gaviria takes victory in Stage 1 of the 2018 Tour de France.
Porte's BMC squad won the day and now the Tasmanian sits in 14th overall, 51 seconds behind his teammate van Avermaet.
"There will be a lot more time lost throughout the GC group before we hit the mountains".
Froome is aiming to join Jacques Anquetil, Eddy Merckx, Bernard Hinault and Miguel Indurain as the only riders to win the Tour five times.
Gaviria's compatriot Rigoberto Uran nearly lost time after being caught in a late crash around 5km from the finish, but he was paced back to the main group by his EF Education First-Drapac team to stay 10th, 35 seconds behind Van Avermaet. "They looked strong throughout, and were rewarded for their efforts with the fastest time, their time of 38'46" taking four precious seconds out of Sky with a ride averaging 54.9kmh.
The other members of BMC are Kiwi rider Patrick Bevin, Damiano Caruso, Simon Gerrans, Stefan Kung and Michael Schar. Van Garderen almost became the second (or sixth) American to wear the yellow jersey.
"I feel maybe even better (than last year)", Porte said. "It's a long way to go, we still have six more hectic days and then we have also got the Alps and the Pyrenees". "It just shows that we are here, too, and let's get it on".
Sagan would have been happy to hold on to it, but the yellow jersey isn't his priority for the Tour, and with the top 59 riders overall separated by just 16 seconds, it was going to take something special from Bora-Hansgrohe to keep him on top.
The only individual time trial of the race comes in the penultimate stage, over a 31-kilometer route from Saint-Pee-sur-Nivelle to Espelette in the Basque country.