The midfielder fired home deep into first-half stoppage time, before top scorer Tom Bradshaw netted his fifth of the season early in the second half to double the lead.
Anthony Forde then put the icing on the cake with his first goal for the Saddlers, striking home an excellent free-kick.
Doncaster failed to force a save from home goalkeeper Richard O'Donnell as the Saddlers recorded their second straight home win.
Baxendale's goal, his first since he netted late on in a 3-0 win at Crewe last September, came from the first shot on target of the entire game.
But, once it had gone in, there only looked like being one winner as Dean Smith's men took control in the second half.
Bradshaw had replaced Ashley Grimes in attack in the only change from the side which drew 0-0 at Gillingham a week ago.
And there was unexpected good news on the bench with Jordan Cook, out since injuring his ankle in pre-season, named among the substitutes along with James Chambers, who had been out for a month with a hamstring strain.
A bright start from the hosts saw Forde twice have shots from the edge of the box blocked in the opening minute, while Bradshaw couldn't quite get a firm shot away after a clever Romaine Sawyers flick.
The Saddlers saw much of the ball but could not fashion much in the way of chances.
Forde again had a shot blocked while Adam Chambers sent an effort high and wide after Doncaster had been forced to bring on Marko Marosi for injured Villa loanee Jed Steer in goal.
Doncaster's only real effort of the half was a James Coppinger shot which flew wide of the post and the game looked destined to be goal-less at half-time, before Baxendale jolted it into life in the third minute of stoppage time.
The Saddlers won a free-kick midway into the Rovers half and, rather than loft the ball into the box, Forde took the option of playing in Romaine Sawyers on the left wing.
Sawyers then pulled the ball back to Baxendale who ook a touch before shooting past Marosi and into the corner.
Doncaster's Theo Robinson drilled a shot narrowly over from distance early in the second-half before the Saddlers, saw appeals for a penalty waved away when Bradshaw appeared to be brought down by Cedric Evina.
Forde drilled a shot straight at Marosi after cutting inside from the left flank.
And it was that area which provided the Saddlers second as Sawyers, after a neat interchange, lofted a cross into the box and which Bradshaw raced onto before slotting a first time finish past the keeper.
The striker had a hand in Forde's brilliant third too, winning the free-kick 20 yards out which the former Wolves wide man swept home via the post for his first Saddlers goal.
That ended the game as a contest, though things almost got even better for the hosts when Mathieu Manset headed narrowly over after coming on as a late substitute.

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