Both of Johnson's TD receptions came in the second half as the Lions (6-3) grabbed the divisional lead over the Bears and the Green Bay Packers, who fell to Philadelphia Sunday.
Johnson finished with six catches for 83 yards. His second touchdown gave him 63 for his career, passing Herman Moore for the club record.
Stafford made good on 18-of-35 pass attempts for just 219 yards with an interception to go along with the trio of scoring strikes while Reggie Bush amassed 105 rushing yards on 14 carries.
Jay Cutler, returning after a one-game injury absence, completed 21-for-40 passes for 250 yards with a touchdown and interception for the Bears (5-3).
He missed the game's final series with an ankle injury.
Brandon Marshall picked up 139 yards with a pair of TDs on seven receptions.
Alshon Jeffery made nine grabs for 114 yards for Chicago.