Lincoln has a 3.98 ERA in 31 2/3 innings this season, striking out 25 and issuing an alarming 22 walks.
"He has been struggling lately," Blue Jays manager John Gibbons said. "He's had some good outings, and then lately he has been struggling."
The Blue Jays did not announce a corresponding roster move, but it will likely be another reliever to help an overly taxed bullpen that was forced to pitch 4 2/3 innings in the series opener. Right-hander Mickey Storey, who was optioned to Triple-A on Aug. 15, could be a candidate.
Left-hander Aaron Loup was placed on the paternity list Friday afternoon, and the Blue Jays have yet to announce a corresponding move for that as well. Right-hander Chien-Ming Wang will re-join the Blue Jays in time to make Saturday's start against the Astros, taking one of the two open spots.
Gregor Chisholm is a reporter for MLB.com. Read his blog, North of the Border, and follow him on Twitter @gregorMLB. This story was not subject to the approval of Major League Baseball or its clubs.