The Championship's top marksman netted a second-half penalty after Marcus Forss had opened the scoring as Brentford guaranteed a third-placed finish for the second season running.
Their points tally of 84 would have sent Brentford up automatically last season, but they will now attempt to avoid the agony of another defeat in the play-offs.
Thomas Frank's side will have the advantage of playing the home leg of their semi-final second, hopefully in front of 4,000 supporters, as they bid to follow Watford into the top flight for the first time in their history.
But the visitors were disrupted by first-half injuries to Cleverley and debutant Joseph Hungbo as Brentford began to dominate.
It stayed goalless until half-time but 55 seconds into the second half Brentford took the lead when Sergi Canos crossed for Forss to convert at the far post.
Toney's big moment arrived on the hour after he was tripped in the area by Francisco Sierralta.
The striker dispatched his trademark two-step penalty to become the first player to hit 30 goals in the Championship since Glenn Murray for Crystal Palace eight years ago.
The son of Paris St Germain and former Tottenham boss Mauricio was handed his debut as a late substitute, but his most notable contribution was giving the ball away to Canos whose shot hit the crossbar.