Charlie Mulgrew's 80th-minute strike was enough to earn his side victory and ultimately promotion.
The centre-back headed home Bradley Dack's corner for his 14th goal of the season to ensure Tony Mowbray's men's stay in the third tier was limited to a single campaign.
Rovers slipped into the third division last May on goal difference and lost their first two games of the season, but former Middlesbrough boss Mowbray has since guided them to just once loss in 33 games since mid-October.
The win means Blackburn remain second in League One, a point behind leaders Wigan with two games to go.