The Russian team, which had set itself the target of making the top 10, finished the Paralympics in eighth place, winning 18 gold, 23 silver and 22 bronze medals - a big improvement on 2004.
"You have displayed a real team spirit and the will for victory, and showed outstanding skills, winning high awards and setting 18 new world records," Medvedev said.
He added that the Russian athletes had inspired thousands of disabled people across Russia, bringing them new hope.
The president hosted a dinner party for the athletes in the Kremlin's Andreyevsky Hall, after which a group photo was taken.
This year, 145 Russian athletes took part in the Games, compared with 84 at the 2004 Athens Paralympics. The medal haul reflected the increased commitment - Russia was 11th in the medal table four years ago, winning 16 gold, eight silver and 17 bronze medals.
The 13th Paralympics ended with the host country topping the overall medals standings with 89 golds, 70 silvers and 52 bronzes. China also had the largest number of athletes at the Games, with 332 of its disabled sportsmen and sportswomen taking part.
Britain took second place, with 42 gold, 29 silver and 31 bronze medals, while the United States came in third (36-35-28).
