Halladay was taking his physical Tuesday morning, sources said.
The status of the other portions of a companion deal that would include the Seattle Mariners is uncertain at this point.
The Phillies have a tentative agreement to acquire star pitcher Roy Halladay in a trade with Toronto, and the former Cy Young Award winner was in Philadelphia on Monday for a physical required to complete the deal.
Philadelphia also is discussing a trade that would send Cliff Lee, another former Cy Young winner, to the Seattle Mariners.
The commissioner's office granted a 72-hour window on Sunday for Toronto and Philadelphia to complete their trade, a baseball official familiar with the negotiations told The Associated Press on Monday. The official spoke on condition of anonymity because Major League Baseball didn't make any announcement.
Halladay took a physical on Monday for the NL champion Phillies, another person with knowledge of the situation said, also on condition of anonymity because no announcement had been made.
Philadelphia could give up pitchers J.A. Happ, Joe Blanton and outfielder Dominic Brown as part of a deal, the person said. Those three players also took physicals in Philadelphia on Monday.
Halladay's agent, Greg Landry, was registered at a Philadelphia hotel, a sign the sides were working on a contract extension, which likely would be necessary before Halladay waives his right to block a trade.
Lee, who like Halladay is eligible for free agency after next season, could wind up going to Seattle, the baseball official said.
The 32-year-old Halladay is the most prized pitcher on the trade market. A six-time All-Star and the 2003 AL Cy Young Award winner, the right-hander went 17-10 with a 2.79 ERA for the Blue Jays last season. He led the majors with four shutouts and nine complete games while throwing 239 innings, second to Detroit's Justin Verlander (240).
Halladay would be a huge addition for the aggressive Phillies, who won the 2008 World Series and repeated as NL champs this year, when they lost the World Series to the New York Yankees in six games.
The Phillies are thought to be a preferable fit for Halladay because they hold spring training in Clearwater, Fla., near his offseason home.
Aware they probably couldn't afford to keep Halladay beyond next season, the Blue Jays shopped their ace before the July 31 trade deadline. The Phillies were thought to be involved in talks involving Halladay at that point, but instead they landed Lee from the Cleveland Indians for four minor leaguers.
Lee was a big reason Philadelphia won its second consecutive pennant, going 4-0 with a 1.56 ERA and two complete games in five postseason starts.
The Blue Jays fired general manager J.P. Ricciardi late in the season and replaced him with Alex Anthopoulos. When contacted Monday by the AP, Anthopoulos declined comment.
The Phillies have been busy this offseason, signing free-agent third baseman Placido Polanco to an $18 million, three-year contract. They also signed Brian Schneider to be their backup catcher, and reserve infielder Juan Castro.
Halladay has been one of baseball's best pitchers for years. He owns a 148-76 career record with a 3.43 ERA.
AP Sports Writers Ronald Blum and Mike Fitzpatrick in New York and AP freelance writer Ian Harrison in Toronto contributed to this report.