Malinga, who was slapped with a suspended six-month match ban earlier this week, has been told to take two days of rest after coming down with the bug.
“Medical reports have ruled him out of the next game and recommended a rest period of 48 hours,” Sri Lanka Cricket said in a statement.
It added that Lakshan Sandakan did not play in the first ODI on Friday at Galle because he had the same virus.
Malinga, 33, took one wicket on Friday, giving away 51 runs in the game which Zimbabwe won by six wickets.
The 80-kilo (176-pound) bowler was disciplined after he pleaded guilty to comparing the country’s sports minister Dayasiri Jayasekera to a monkey for saying national cricket players were too fat and unfit.
Jayasekera has given national players three months to improve their level of fitness or get booted out.
He said the entire team selected to play against Zimbabwe were below the internationally accepted fitness level.