.The Millers dominated large periods of the game and led twice through Kieffer Moore.
Bury, who had manager Lee Clark sent to the stands at half-time by referee Christopher Sarginson, responded twice through Jermaine Beckford and Nathan Cameron before Towell's strike won it for the home side.
Rotherham's early pressure paid off in the 20th minute when Moore finished clinically after bringing down Will Vaulks' cross and slotting past Joe Murphy.
Jon Taylor should have made it two after he rounded Murphy but the winger's shot went into the side-netting.
The miss was punished instantly with Beckford converting at the near post from Ryan Lowe's centre in the 34th minute.
Rotherham were back ahead nine minutes into the second half when Moore headed in from Taylor's left-wing cross.
Bury equalised again in the 67th minute with Cameron powering in Michael Smith's flicked header.
But Towell latched on to a loose ball on the edge of the box and drove into the bottom corner to secure back-to-back wins for Rotherham.