Earlier in the game, Clayton fouled a pitch from Yankees left-hander Andy Pettitte off his left foot, but the 37-year-old veteran remained in the game. By the ninth, though, Toronto manager John Gibbons said Clayton was having difficulty walking.
Gibbons said the Jays will know more about the extent of Clayton's injury on Wednesday, but added that it's likely the shortstop will sit out the next few games. In the meantime, Gibbons indicated that Toronto, which is currently carrying only 12 position players, would probably have to call someone up to help fill in.
"He could hardly walk," said Gibbons, who added that the injury became progressively worse as the game wore on. "I would think [he'll be out] a couple days. There's a chance it could be broken. You never know. They've got to check it out."
After pulling Clayton, who is hitting .243 with one homer and nine RBIs in 38 games, the Jays replaced him with John McDonald at short in the ninth inning. McDonald started at third base on Tuesday in favor of Troy Glaus, who was a late scratch from the lineup due to a foot injury of his own.
Glaus has been bothered by a bone spur in his left foot all season, and he missed Sunday's game in Minnesota as a result of the ailment, which cost him 14 games during a stint on the 15-day disabled list in April. The 6-foot-5 Glaus has also had occasional issues with his left hamstring, which was the case again prior to Tuesday's game against the Yankees.
Due to being short-handed on the bench, though, Gibbons had to turn to Glaus when Clayton needed to be removed. After optioning utility man Ryan Roberts to Triple-A Syracuse on Monday, the Jays' bench on Tuesday consisted of catcher Sal Fasano, outfielder Matt Stairs and Glaus.
"Troy said he could go," said Gibbons, when asked why Glaus entered the game in the ninth. "We had to [rest] him earlier in the game because of his hamstring. With the foot problem he's got, he's overcompensating and beating up his legs pretty good."
Gibbons said that Glaus, who is batting .278 with eight homers and 24 RBIs this year, would most likely be back in the lineup in the finale of the three-game set against the Yankees on Wednesday.
"You hope so," said Gibbons, whose club has had 10 players land on the DL this season. "He could probably use [a day off], but desperate times call for desperate measures."
Jordan Bastian is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.