Cedric Bakambu finished second with a stunning strike in the 27th minute after a goal was disallowed for offside in the opening time.
The 62-year-old didn't exclude himself from the solution after leaving RB Leipzig eight weeks ago.
Several of those who tested positive for the virus have since recovered and Flamengo were able to begin Wednesday's match with seven of their usual starters.
The game was played behind closed doors at the Menorah Mivtachim Arena in the coastal city of Tel Aviv.
Zidane is likely to bring either Isco or Luka Modric into his starting 11 to replace Kroos, although the doubt remains whether he will use a 4-4-2 with a midfield diamond formation that helped Madrid beat Betis at the weekend, or the 4-3-3 he fielded away to Real Sociedad in his side's league opener.
The result at Rio de Janeiro's Maracana stadium, which came less than two weeks after Independiente whitewashed Flamengo 5-0 in Quito, guarantees the defending champions a place in the knockout phase.
Shanghai will face Shaanxi on Sunday, while Tianjin's opponents on Monday will be Jiangsu. Enditem
CHENGDU, China, Oct. 1 (Xinhua) -- It took Shandong just one quarter to seal their opening victory in the Women's Chinese Basketball Association (WCBA) league new season by overwhelming Daqing 101-51 here on Thursday.
Vital performers such as Robert Lewandowski and Thomas Mueller demanded new faces after admitting to be exhausted after an energy sapping 2019/2020 season.
The Nerazzurri made a dream start just 28 seconds into the game, as Romelu Lukaku broke the deadlock from Achraf Hakimi's assist.
Everton made it three wins from three games after Dominic Calvert-Lewin and Richarlison's penalty, given by the VAR for handball, gave them a 2-1 win away to Crystal Palace