Dean Saunders' Championship strugglers came into the game on the back of three consecutive home victories, but were more than matched in all departments by Martin Allen's League One outfit.
Hughes was gifted the opening goal when Rovers failed to deal with Alan Sheehan's 37th minute free-kick and the midfielder settled County nerves from the penalty spot with 20 minutes to play.
Giles Barnes passed up Doncaster's clearest opportunity when he shot over from close range moments before Hughes' second, while James Hayter toiled without reward in attack as El-Hadji Diouf watched 80 minutes from the substitutes' bench.
Mali international forward Mamadou Bagayoko made his Doncaster debut as one of four changes from the Rovers side that beat Barnsley on Monday, while Damion Stewart was selected for his Notts County bow in defence after joining on loan from Bristol City.
County enjoyed their first opening when Lee Hughes got the better of Rovers defender Sam Hird to find strike partner Karl Hawley, who shot narrowly past the post after 13 minutes.
The visitors settled impressively and Lee Hughes was inches away from breaking the deadlock with a header from full-back Julian Kelly's sublime cross.
Doncaster midfielder Brian Stock carelessly ceded possession inside his own half with 23 minutes gone, allowing Alan Judge to advance for the Magpies and drill wide from 20 yards.
Judge then engineered another opportunity at the end of some cute work in the inside right position, but home goalkeeper David Button reacted sharply to parry clear.
At the other end, Barnes spurned a free header from James Coppinger's 32nd-minute centre, nodding into the grateful arms of Stuart Nelson.
It was a miss Saunders' side would regret shortly afterwards when some sloppy defending saw Sheehan's right-wing delivery bounce loose at the back post for Jeff Hughes to steer home.
Kyle Bennett brought a fine save from Nelson with a swerving, dipping drive as Doncaster made a brighter start to the second half.
Lee Hughes had an effort deflected wide as Notts County continued to threaten on the break, but Doncaster were making the running and Hayter had a penalty appeal rejected when he went to ground under pressure from Stewart shortly after the hour.
Then Coppinger almost found a fortuitous equaliser when his arching cross had Nelson backpedalling to tip around the post.
The resulting corner was only partially cleared and when Coppinger sent the ball back into the area it fell to Barnes, who blazed wastefully over from 10 yards.
And once again, a Barnes miss was followed by a County goal as Bennett hacked through the back of Sheehan in the box and Jeff Hughes withstood some kidology from Button to coolly find the corner.
Bennett had the chance to redeem himself when Hayter played him into space in the County area, but he slashed wide before Diouf followed up a booking for dissent by heading past the post from fellow substitute Martin Woods' free-kick.