Froome slipped behind and Dumoulin moved from third to second overall at 1:59 minutes behind Thomas.
Chris Froome has crashed following the brutally hard 17th stage of the Tour de France after police mistook him for a fan on the way down the mountain.
Team boss Dave Brailsford said they will now plan to make sure Froome joins Thomas on the Tour de France podium: "He's not out of it necessariy, there's a big mountain day to come, and the time trial". We don't feel unsafe, it's just unfortunate sometimes but I think everyone is doing the best they can.
This stage in particular held a special place in Martin's heart after having his first brush with the Tour de France in these same mountains nearly 20 years ago.
"It was a tough day, an intense day, but I've got no regrets", Froome said.
"Froomey said on the radio @ maybe 5K or 4K to go that he wasn't feeling super", Thomas said.
1 person killed in Northern California wildfire
Teague says staff and volunteers were mindful of the brightening glow of the fire burning nearby in the hills above Redding. The blaze, which is raging west of the park, has burned 45,911 acres and is 29% contained, Cal Fire said Friday morning.
Quintana, who started the day more than four minutes back in the general classification, hauled himself back into the top five with the second Tour stage win of his career.
Thomas remains in the overall race lead with an advantage of 1min 39sec to Froome.
"My throat, nose and eyes were burning afterwards, but I think quite a lot of riders were in a similar situation so I think we were all grateful for the temporary neutralisation just to have a couple of kilometres to clear our eyes, nose and throat out and then the race continued again".
At one point it looked like going the other way, with Froome following an attack by LottoNL-Jumbo's Roglic midway up the climb, leaving Thomas to sit on the wheel of Dumoulin as the Dutchman worked to shut down the move.
Gilbert, who rides with the Quick-Step Cycling team, was descending the Col de Portet-d'Aspet and leading the breakaway when he took an aggressive line on a turn.
Philippe Gilbert of Belgium receives care during the 16th stage of the Tour de France. Instead, on arriving back at the bus, he praised the performance of his team-mate Geraint Thomas, admitting he was the stronger rider and vowing to work with him for the rest of the race.
"The last two or three days I have felt pretty good", he said.
The latest roadside drama erupted only 30km into Stage 16 when the protesters dragged hay bales onto the road, narrowing the space for the oncoming peloton.