Toney netted with a 10th minute penalty to end a run of three successive away defeats for Thomas Frank's side.
Brentford moved above Watford and Swansea City on goal difference as the race for automatic promotion to the Premier League heats up.
Watford and Swansea can go back ahead of Brentford if they avoid defeat against Cardiff City and Luton Town respectively this weekend.
Leader Norwich City is 10 points clear of Brentford and looks certain to secure an immediate return to the top-flight after last season's relegation.
Brentford's intense early pressure was rewarded when Tom Trybull's loose pass was seized upon and Tarique Fosu's trickery forced Darragh Lenihan to concede the penalty.
Toney took a two-step run-up before clinically dispatching the penalty into the bottom corner.
Blackburn's Bradley Dack shot just wide from a narrow angle in the second half.
But Toney reminded Rovers of his threat with an audacious 50-yard free-kick that landed on the roof of the net.
Brentford finished strongly and Blackburn keeper Thomas Kaminski made an outstanding save to deny Marcus Forss from close-range before Toney hit the side-netting.