Chris Brown tapped home his eighth goal of the season just after the half-hour mark to settle a passionate South Yorkshire tussle and extend Rovers' unbeaten run to four games.
Leon Best had earlier missed a gilt-edged chance for the Owls who started the game brightly but lost their way after Brown broke the deadlock.
Rovers defended well after the break, soaking up everything Wednesday threw at them to keep a third clean sheet in four games, move eight points clear of the drop zone and complete a league double over their local rivals.
Wednesday came bursting out of the blocks but it was boyhood Sheffield United fan Billy Sharp who registered the first serious attempt on goal, his 20-yard effort deflecting just over.
At the other end Sam Johnstone got down well to save Lewis Buxton's drilled effort from the edge of the area after the Manchester United loanee had punched clear, before Best inexplicably missed the target from point blank range after Jeremy Helan got clear down the left.
Rovers were under the cosh a little as the energetic Owls dictated the early tempo.
But the home side still looked a threat going forward, particularly when James Coppinger joined in the attacks. The makeshift right back went close to breaking the deadlock, latching onto David Cotterill's short free kick but blasting straight at Chris Kirkland.
The hosts then grabbed the lead just after the half hour. Richie Wellens was allowed the space to play in Sharp, his shot was blocked by Kirkland but the rebound fell kindly for Brown who gratefully tapped home.
The goal seemed to sap the confidence and life out of Wednesday as Rovers ended the half on top.
In stark contrast to the first period, the second half got off to a subdued start.
That was until Chris Maguire turned neatly on the angle of the box but his piledriver was expertly beaten away by the impressive Johnstone.
Rovers had an element of control and they went close to doubling their lead when Sharp flicked on Cotterill's inswinging free kick but Kirkland made a point blank save.
Johnstone again had to be alert to divert Best's flicked header and substitute Sam Hutchinson then headed over from a corner as the visitors raised the tempo in search of an equaliser.
Doncaster continued to defend well during the closing stages, although there was an element of huff and puff about Wednesday's forward play.
Cotterill almost sealed it when his late free kick was superbly tipped wide by Kirkland but Brown's tap-in ultimately proved to be the difference between the sides.