Rovers made a lively start and Lewis Guy broke on the left and crossed for Leo Fortune-West who could only produce a weak shot which was easily saved.
Two escapes followed for the visitors, first a 15-yard drive from Mark Jones that flew wide and then a cheeky back-pass from Nick Fenton that caught goalkeeper Andy Warrington unawares and had him racing back to clear his lines.
Wrexham debutant Robbie Foy, on loan from Liverpool, let Rovers off the hook when he should have scored but hit his close-range shot too high and Danny Williams also lifted his shot over the bar from the edge of the area.
Rovers had their best chance just on half time when James Coppinger went through on the right and crossed for the unmarked Michael McIndoe but his header was off target.
Coppinger missed another good opening, shooting wide when McIndoe repaid the compliment and put him through.
Wrexham turned up the pressure after half-time as Warrington had to hold a header from Andy Holt, turned a Darren Ferguson shot around the post and saw a Mark Jones shot miss the post by inches.
At the other end Guy should have given Doncaster the lead but stumbled when about to shoot and Coppinger missed an open goal.
But Hughes spared Rovers' blushes with his late goal.