Trainers noticed the five-year-old mare had "a little heat" in her right front ankle following the workout, Porter said in a statement on his Fox Hill Farm website.
Havre de Grace, the Kentucky-bred winner of the Grade I Woodward Stakes last year, was seen by veterinarians on Monday and Porter was given the bad news.
"Unfortunately, we didn't get a positive prognosis for continuing her racing career," he said.
Havre de Grace won nine races in 16 career starts and won nearly $2.6 million. She won five of seven trips to the starting gate in 2011 and won U.S. Horse of the Year honours.
The Larry Jones-trained bay daughter of Saint Liam won her lone race this year, the $150,000 New Orleans Ladies Stakes, by four and a half lengths at Fair Grounds Race Course.
"Owning Grace through her racing career has been the highlight of my time in horse racing," said Porter. "She was a wonderful, wonderful racehorse, and I feel confident she'll be an equally wonderful broodmare.
"Thanks, Grace, for all you gave us, and here's to a long and enjoyable retirement."