The spacecraft landed slightly ahead of schedule at 0802 Moscow time, Roscosmos said on its website.
"The crew feels well after returning to Earth," the space agency said.
Live footage on the websites of NASA and Roscosmos did not show the landing of the astronauts' capsule due to thick fog in the Kazakh steppe.
NASA said that all the search and recovery helicopters had arrived at the scene and were preparing to extract the crewmembers.
When the astronauts blasted off in June, they were one of the least experienced crews ever to join the International Space Station - only Gerst had been on a space mission before, in 2014.
The first significant incident came in August when astronauts detected an air leak in their Soyuz spacecraft, which was docked to the orbiting space laboratory.
They sealed the small hole successfully but Russia launched an investigation and its space chief Dmitry Rogozin suggested it could have been deliberate sabotage carried out in space.
Rogozin said that investigators ruled out the possibility the default was introduced during the spacecraft's manufacture.
Prokopyev and fellow Russian Oleg Kononenko last week carried out a gruelling space walk lasting almost eight hours to locate the hole from the outside and record and bag evidence.
The hole was in a section of the astronauts' spacecraft that was to fall away and burn up in the atmosphere as they landed, hence the need to carry out the probe in space.
During the space walk, Kononenko said there was some kind of black and yellow "furry" deposit that looked like a "spider" around the hole, but no conclusion has been made public.
The crewmembers were bringing back the evidence to Earth.
Their landing back on Earth was originally planned for December 13 but the schedule was put back after the October failure of a Soyuz rocket carrying the next crew -- the first such aborted launch in the post-Soviet era.
Russia's Aleksey Ovchinin and US astronaut Nick Hague took off for the ISS on October 11 but their Soyuz rocket failed minutes after blast-off, forcing them to eject and make a harrowing emergency landing.
At the time Gerst wrote on Twitter that the astronauts' survival showed "what an amazing vehicle" the Soyuz rocket is.
"Spaceflight is hard. And we must keep trying for the benefit of humankind," he wrote.
The first successful launch of astronauts since the October accident took place on December 3, carrying Kononenko, Anne McClain of NASA and David Saint-Jacques of the Canadian Space Agency.