Honest Ed and Tecumseh were part of the parade on Pennsylvania Avenue.
This is Honest Ed's second inauguration, having taken part in Obama's historic 2009 event.
"He's our veteran, whereas I've never been," Sgt. Jim Patterson, who rode the horse in the parade, said earlier this month.
Staff Insp. Bill Wardle said he and Patterson were there as guests of an American police unit.
"If it wasn't for that there would not be Canadian representation in the inaugural parade," he told host Matt Galloway on CBC's Metro Morning.
Wardle said the Toronto police are well respected south of the border.
"When the Americans look at us, they really see a high level of skill, and we really do share our knowledge," he said. "We have a lot of American units coming up here that we train."
In another interview earlier this month, Wardle talked about the symbolism of these particular horses.
"I thought it would be great to take Honest Ed — who was named for a man who was so important to Toronto over the years — and Tecumseh, a native aboriginal chief who was instrumental in helping Canada remain a country, but who was also seen as a hero in the United States," Wardle said.
The late Ed Mirvish was a Toronto businessman renowned both for his landmark discount store Honest Ed's and for his key role in revitalizing the city's theatre scene.
For the Mirvish family and department store staff the inauguration is also a great honour.
"We couldn't be more pleased," Russell Lazar, manager of the department store, said. "[The horse] is part of our family."
The crowd for Obama's inauguration is expected to be a fraction of what it was four years ago, but hundreds of thousands are still expected to attend.