The Russian, who won in 2014, was third at the time of the incident on Friday with two wins from the five stages so far.
"A 60-year-old man from South Africa, who was watching the race in an unsecured area... was hit by a race truck (#518 Andrey Karginov)," organisers said in a statement.
"The competitor was excluded from the rally by the jury of commissioners for not stopping to attend the injured spectator," they added.
The spectator suffered a broken femur and was flown to hospital in Arequipa.
The motorsport.com website reported that Karginov's truck drove over the spectator's left leg and quoted Kamaz team boss Vladimir Chagin as saying the exclusion was "very harsh".
He said the driver had been unaware of what had happened until the end of the stage.
"As he was driving up one of the ascents, there was a group of five spectators in the path of the truck. Four managed to clear off but one tripped in the sand and his leg was caught under the rear wheel of the truck," said Chagin.
"Andrey naturally didn't see this -- it was an ascent and all you can see through the windshield is the sky and the top of the mountain."
Saturday is a rest day for Dakar competitors. The rally, staged in South America since being switched from Africa in 2009 for security reasons, ends in Lima on Jan. 17.
(Reporting by Alan Baldwin in London, Editing by Ken Ferris)
