The peloton kept the gap to the break between 90 seconds and three minutes for much of the running, through the climb and the descent ahead of the flat run to the finish.
Quintana increased his 54-second advantage entering the day to 3 minutes, 37 seconds after leading the charge up the last of three ascents while Froome struggled to pursue.
Esteban Chaves of Colombia remains third overall, 20 seconds adrift of Froome.
Froome, the Team Sky rider and Tour de France victor, was caught napping in the opening minutes of the mountainous 120 kilometres stage from Sabiñanigo to Formigal.
Chris Froome's Vuelta a España imploded in dramatic fashion yesterday as his team-mates deserted him after a spectacular attack from Nairo Quintana and Alberto Contador.
Daniele Bennati made a dash for the line two kilometres from the finish, and some hesitation in the chasing pack almost allowed the Italian to take the stage before he was swept up in the final few hundred metres. I saw Contador was starting to fade and I had to follow Nairo.
Froome's hopes could rest on Friday's individual time trial from Xabia to Calp, with two mountain stages also to come before the finale in Madrid this weekend.
Meanwhile, Andre Greipel won the opening stage of the Tour of Britain as Mark Cavendish fell in a crash on the final corner. "Jasper and Emiel rode like champions today and were rewarded with the jersey for Bovenhuis".
The BMC rider claimed the 156.4km 16th stage from Alcaniz to Peniscola in a time of 3hrs 21mins 18secs ahead of German duo Rudiger Selig and Nikias Arndt.
The day's breakaway worked well and provided Bovenhuis with the platform to take maximum points at the three Yodel Sprints in Glasgow, Kilmarnock and Dalmellington.
"I've done six weeks of training after the Tour de France and this race is really important towards the next goal (October's Road World Championships)".