President Vladimir Putin signed a decree reinstating Mishustin as the head of government, nearly three weeks after the prime minister announced on television he had tested positive for coronavirus.
Mishustin checked himself into hospital and his deputy was named interim prime minister, but he continued to participate in meetings via video-link wearing a suit and tie.
The 54-year-old former tax chief was appointed prime minister in a surprise government shake-up earlier this year but had little time to make an impact before the coronavirus pandemic hit.
His reinstatement came after health officials reported 9,263 new infections in Russia over the last 24 hours, bringing the total to 299,941, the second-highest in the world after the United States.
Mishustin was just one of several high-ranking Russian officials to have been infected, including the ministers of culture, education and construction, as well as Putin’s spokesman Dmitry Peskov.
The prime minister said Monday that Russia had stopped the growth of new infections, but cautioned that the situation remained “difficult”.
He credited a nationwide lockdown and “systematic work” over the past two months for slowing the rate of new infections.
The Kremlin last week eased nationwide anti-virus measures imposed in March and Mishustin said Monday that dozens of regions throughout the country were ready to gradually lift lockdown orders.
Tuesday’s tally saw new cases fall below 10,000 for the fourth day in a row, after Monday’s count saw new infections under 9,000 for the first time since the beginning of May.
A majority of infections in Russia are centralised in the capital, which has extended its lockdown until the end of May, with residents only allowed to leave their homes for brief trips to a shop, to walk dogs or to travel to essential jobs with a permit.