Abayomi made the disclosure through his Twitter account on Friday night.
He did not, however, provide additional information about the deceased's sex, age, nationality or medical conditions.
He added that 139 new cases of COVID-19 infection were confirmed in Lagos on May 21, bringing the total number of confirmed cases in the state to 3,109.
The commissioner noted that, on the same day, 13 patients with COVID-19; four women and nine men were discharged from the state's isolation facilities after their full recovery.
"This brings the total number of # COVID-19 patients discharged to Lagos to 662" he said.
The Nigeria News Agency (NAN) reports that Lagos has 2,383 active cases, two have been evacuated from Nigeria, while 16 have been transferred to the Ogun and Ondo states.