Bowery’s header right at the end of the first half proved to be the difference between the Sky Bet Championship and League Two teams at the New York Stadium.
Cambridge’s Keith Keane had the first shot of the match but his 25-yard effort was dragged wide.
Former Rotherham loanee Jordan Slew then blasted over the bar from inside the box as the visitors made the brighter opening.
Rotherham responded and striker Matt Derbyshire almost had a stroke of fortune as he deflected a Joe Newell cross with his head just over the bar.
It took until stoppage time at the end of the first half for the deadlock to be broken when Bowery got free at the back post to head in the impressive Newell’s centre.
Rotherham had a host of chances to extend their lead in the second period.
Bowery continued to look lively and after being found by Aidy White cut inside and curled an effort wide of Chris Dunn’s far post.
Derbyshire nodded a White cross just wide as the difference in quality between the two teams became more apparent.
Conor Newton, who left Rotherham in the summer, fired a late shot on target but Kelle Roos pushed it away.