The capsule -- ferrying Expedition 22 Commander Jeff Williams and Flight Engineer Maxim Suraev -- landed in the vast steppe near the town of Arkalyk in northern Kazakhstan as planned, Russia's Mission Control said.
"The descent capsule of the Soyuz TMA-16 ... has landed," an announcer at Mission Control outside Moscow said to applause from space officials and controllers. "The capsule is lying on its side."
The capsule, charred on re-entry, ended its three-and-a-half-hour ride to Earth in a puff of dust after activating its boosters to cushion the touchdown.
"The crew is safe. They say they are in a great mood," a Mission Control official told Reuters by telephone several minutes later, while rescue teams were opening the hatch of the capsule and preparing for medical checks on the crew.
The expedition, which is numbered 23 and is led by Kotov, will expand to a six-member crew on April 4 after three others -- Russians Alexander Skvortsov and Mikhail Korniyenko and U.S. astronaut Tracy Caldwell Dyson -- arrive at the ISS aboard a Soyuz spacecraft.
Russia will ferry all crews to the ISS aboard its single-use Soyuz spaceships after U.S. space agency NASA mothballs its shuttle fleet by the end of this year.
Earlier this month Russia announced a halt to space tourism to free capacity for ISS flights. It plans to double the number of launches to four this year as permanent crews of professionals aboard the expanded ISS are set to rise to six.