Many other facilities including parks, beaches, libraries and museums also reopened across the country, while millions of public sector employees returned to work.
Bars and nightclubs remained closed. Restaurants and cafes, reopening for the first time since March 16, must operate under strict rules.
Domestic flights also resumed between a limited number of cities as an inter-city travel ban was lifted.
The national flag carrier Turkish Airlines said its first plane since the ban took off from Istanbul to the capital Ankara at 0700 GMT Monday.
International flights have been suspended until June 10.
Turkey, with a population of 83 million, has recorded more than 4,500 virus-related deaths.
The government has boasted of its success in handling the outbreak and avoiding becoming a virus hotspot such as Italy or the United Kingdom.
Officials say the pandemic is now under control, but have repeatedly warned citizens to respect social distancing rules and wear masks outside.
The Grand Bazaar, an Istanbul landmark situated on the historic peninsula also home to tourist sites such as the Hagia Sophia museum and the Blue Mosque, shut down on March 23.
It has been the longest closure in the market’s 559-year history that did not involve fires or earthquakes.
The bazaar reopened under strict rules laid out by the health ministry that include the mandatory use of masks and a limit on the number of customers allowed into shops.
“You see some of the stores have premises with 15-square-metre (160-square-feet) areas and a maximum of two shoppers will be allowed inside,” Fatih Kurtulmus, head of the Grand Bazaar’s board, told AFP last month.
The bazaar — which was built in 1455 just two years after the Ottomans seized Istanbul, then known as Constantinople — is home to almost 3,000 shops where more than 30,000 people work.