The stage was won by French sprinter Bryan Coquard, catching Danish rider Mads Pedersen right on the line at the rustic beach resort of Xeraco with its protected marshes.
Pogacar of Team UAE, who rarely falls heavily, has won five Tour de France titles and a Giro d'Italia and was targeting his first overall victory in the Spanish 21-day race.
The Slovenian tumbled to the tarmac after swerving suddenly on an innocuous stretch of road, losing control, flying head-first over his handlebars and landing on his shoulder and face.
With his entire team stopping and waiting, the peloton at first slowed down but then carried on after Pogacar tried to remount a couple of minutes later, but cried out "no" and winced in pain when he touched his bike.
He was led to an ambulance as his teammates set off up the broad and freshly laid dual carriageway towards the finish line at Xeraco, near Valencia, with the look of a defeated army, nine minutes off the pace.
Pogacar had been leading Mas by three minutes and 50 seconds. This marks the first time the 27-year-old has failed to finish a Grand Tour.
His team confirmed he had suffered a "displaced left clavicle fracture" and a "cervical fracture", as well as a concussion.
"Fortunately, (he has suffered) no other major injuries and no neurological fallout," UAE's team medical director Adrian Rotunno said in a statement.
"He will require clavicle surgery, which will be delayed due to concussion precautions.
"Tadej remains under the care of our medical team, and we'll provide further updates following the surgery."
Mas left in lead
Mas is a minute and 11 seconds ahead of Austrian Felix Gall, and former champion Primoz Roglic is third at one min 33 seconds back.
In July, Pogacar joined an elite club of five-time Tour de France winners with Jacques Anquetil, Eddy Merckx, Bernard Hinault and Miguel Indurain.
He is the youngest rider to have won five Tours, more than a year younger than Merckx, and is the first person to finish on the podium seven years running.
He is also the only rider to have been on the podium in nine consecutive Grand Tours.
Saturday's stage winner, the 34-year-old Coquard, registered his first career Grand Tour win.
"I've waited 13 years for this; I've been second many times. I'm very proud of the work I've put in to get here. I'm fast again," he said after taking the podium.
The peloton faces a mountain summit finish on Sunday with a long 22km ascent of a classic Vuelta slog up the Alto de Aitan averaging nearly six per cent gradient.
Monday will be a rest day with two weeks of racing remaining.