Aru went from six seconds ahead to 18 seconds back, losing 24 seconds to the group with Froome in the short 500-metre uphill sprint.
“I was a little too far behind,” said Aru. “I was in the second group behind, I made a huge effort to get up there and I paid.
“At 1.5 kilometres remaining, the group was already broken up. I was behind, I closed it, but it was too late.”
Australian Michael Matthews (Sunweb) topped the stage results.
Froome was the most attentive of the grand tour riders. He finished seventh in a group with Daniel Martin (Quick-Step Floors) and Rigoberto Urán (Cannondale-Drapac), while Simon Yates (Orica-Scott) and Romain Bardet (Ag2r La Mondiale) lost five seconds and Aru, 24 seconds.
“It happens [to find yourself in a bad position]. They are situations in the race, it’s important to continue and not lose my path,” Aru added.
“I saw that [the times when coming over the finish line], it’s not a lot, but then it’s nothing to laugh at. The race, though, is still pretty much open.
“Logically, I’d prefer to keep it, but yeah, the last week will be very demanding, so not everything is lost.”
The 27-year-old from Italy’s island of Sardinia took the yellow jersey from Froome two days ago when the race finished at Peyragudes. Froome lost 22 seconds in the last 200 metres.
“When it kicks off at that speed, the last 500m à bloc, it’s hard and Van Avermaet or Gilbert are used to it,” Astana Team Manager Giuseppe Martinelli added.
“I saw that he was immediately behind, but it’s useless to say move up, move up when they are going that strongly. If you take the climb at the back of the group, it’s easier to be caught out, but then 18 seconds seems like a lot, but on the climbs he can recover it.”
Astana admits it is suffering from a weakened team. Helper Dario Cataldo and co-captain Jakob Fuglsang abandoned in the last few days due to fractured bones.
“I’m sorry that he lost time, but it’s not a drama. I think that if today was an off-day for us, then it could happen to the others in the days coming up,” continued Martinelli.
“I believe in Fabio for the Alps, and of course, tomorrow, the race will be in Sky’s hands and we can be calm.”
Aru said of being down two helpers, “It’s just something that happened, but we are going to go ahead all the same in this Tour.”