Kelderman came down, suffering a fracture to a finger on his left hand that ended his race, and brought Thomas and several others down as well.
Thomas and Landa bravely got back on their bikes to complete the stage.
The Welshman battled all the way to finish five minutes behind stage winner and new race leader Nairo Quintana of Movistar but dropped to 17th overall, while Landa tumbled down the standings after finishing over 26 minutes in arrears.
"We were all racing, then someone in front of me hits a motorbike. My shoulder popped out," Thomas said.
"I felt good but then I crashed, and my race was over.
"It's ridiculous and shouldn't happen. It could have been a lot worse.
"We lost five minutes but I felt like I lost three or four of those on the side of the road.
"There are still stages to go for and we might still be able to move up into the top 10 or better."
It is not the first time in recent years riders have suffered directly as a result of incidents with motorbikes involved in the race.
At last year's Tour de France, organisers re-set the stage times for Australian Richie Porte, Britain's Chris Froome and Dutchman Bauke Mollema after they crashed into a motorbike on Mont Ventoux.
On the race's 100th edition, Giro organisers were feeling less charitable - although the general feeling in the peloton Sunday was one of anger.
"I don't know what the stupid motorbike was doing there," said Dutchman Tom Dumoulin, who has been left without teammate Kelderman, notably for the decisive third week of the race.
Although he battled on the climb to finish third at 24sec behind Quintana and move up to third overall, trailing the Colombian by 51sec, his race almost ended too.
"I'm so disappointed. I could just (manage to) avoid it, I saw it at the last moment but I was lucky that I was two centimetres to the right of Wilco.
"They say it happens but it shouldn't happen." Sky boss Dave Brailsford rallied his troops and vowed they will "fight on". But he added: "The moto shouldn't have been there but, equally, I'm sure the guy driving it knows that too.
"We leave it at that, but we have to go back and ask why it happened."
Monday is a rest day in the race, which resumes Tuesday with a stage 10 time trial over 39.8km in the Sagrantino wine-growing region.