The Subaru Impreza entry of Vaclav Kopacek and Tomas Singer left the road and collided with the fans, who organisers said were standing in a "forbidden zone" on the 21.40-kilometre Halenkovice stage.
The stage was neutralised then the decision was taken to bring an end to the Intercontinental Rally Challenge rally.
Juho Hanninen therefore takes the win by 1:47 and earns full points in the standings.
"It was extraordinarily sad end to what was proving an exciting rally," said Eurosport commentator Carlton Kirby.
Before the stage was neutralised, Jan Kopecky dropped out of the race from second place with engine failure, meaning Hanninen should have easily claimed victory anyway had that stage stood and the two remaining stages been run - barring a mechanical issue.
The local hero started the stage 16.2 seconds behind Hanninen.
"I don’t know what has happened but only a few kilometres from the start he was at the side of the road," said Hanninen.
"It looks like it was something technical because he has stopped and is not coming. Now we have to find the rhythm again because it’s not easy any more after being in a big fight for the last two days."
Tomas Kostka had cut the gap to Kresta to 1.8s after going almost seven seconds faster than his fellow Fabia driver through the second running of the stage.