More than 7.6 million registered voters can choose who will win the remaining 125 seats up for grabs.
The results are expected next week.
As voting got underway, free masks were distributed at voting stations in line with the “One Malian, one mask against COVID-19,” campaign.
The campaign was announced by the presidency in March as plans for the election went ahead.
“The mask is reassuring and makes it possible to avoid the spread of the disease COVID-19,” said Abdoulaye Traore, who voted in the Bozola district of the capital Bamako.
Fatoumata Diallo said she was “happy to be able to vote with a mask,” adding that she could complete her civic duty without endangering herself and others.
Hygiene measures in place include hand-washing kits at every polling station, with alcohol hand sanitizer available.
Social distancing regulations are in force, but these aren’t always adhered to, a DPA reporter said.
This second round of elections is going ahead despite Mali reporting 171 cases of COVID-19 and 13 deaths from the respiratory disease caused by the highly contagious coronavirus.
The first round took place on March 29, just four days after the kidnapping of Soumaila Cisse, a former presidential candidate and leader of the Union for the Republic and Democracy (URD) opposition party.
Cisse was kidnapped on the campaign trail and to date, no one has claimed responsibility and he has not yet been released.
He was nevertheless elected as a representative for the constituency of Niafunke in the region of Timbuktu, the area where he was kidnapped.
(dpa/NAN)