"He's out. He's probably out for the season again," manager Ryan Neslen said Tuesday.
The 34-year-old striker aggravated a calf problem last week, the latest in a line of niggling injuries since he returned midway through the season after a lengthy absence due to knee surgery.
Koevermans, whose US$1.66-million contact expires at the end of the year, has seen just 78 minutes action this year, with only one start.
When healthy, the big Dutchman has been a force. He had eight goals in 10 games in 2011 and nine in 16 last season.
But he has managed just 22 starts in his time here.
Toronto, which has just four league games remaining, has said it plans to go after two new designated player strikers in advance of next season. And with midfielder Matias Laba already on the books, that would leave Koevermans out in the cold.
"It's a shame. I feel bad for Danny," Nelsen said of his injuries. "I feel bad for everybody because we needed him."
"Mentally it must be hard as well," he added. "When you know your time's running out and you're in the twilight of your career, when you get an injury at that age, it mentally has a double, triple impact on you. Because when you're young, you always feel like you've the world left in your career. But when you're old, you know you don't have much time."
Nelsen said he would sit down with Koevermans at the end of the season to talk about the future.
Striker Robert Earnshaw did practise Tuesday, easing back into play after a slight hamstring problem.
"We might get him for the weekend but we're not sure," said Nelsen.
Toronto (4-15-11) hosts D.C. United (3-20-6) on Saturday.
The Toronto manager says he has not yet decided whether to appeal his and assistant manager Fran O'Leary's weekend ejections.
If he skips the appeal, both will sit out Saturday's game with assistant coach Jim Brennan running the sidelines.