Bowery headed in Paul Taylor’s corner three minutes into added time and ran to manager Steve Evans to celebrate after coming on as a substitute for new signing Jonson Clarke-Harris.
A second-half Steve Cook header had earlier handed Bournemouth a lead, after the hosts missed a host of earlier chances to go ahead.
Rotherham manager Evans had started with a new strike force of Clarke-Harris and former Leeds and Norwich man Luciano Becchio, both signed on deadline day, but the duo failed to trouble Bournemouth’s stubborn defence.
Clarke-Harris came closer of the two to a debut goal in the 24th minute when he raced on to a through ball from Paul Taylor, only for Bournemouth goalkeeper Lee Camp to burst off his line and blast the ball clear.
Becchio and Clarke-Harris were brought in to cure Rotherham’s chronic goal shortage, as Rotherham had only scored twice in their first five league matches.
But the duo failed to trouble a comfortable Bournemouth defence, and both were substituted within 55 minutes.
Bournemouth poured forward themselves in the first half but struggled to dismantle Rotherham’s back line. Marc Pugh and Charlie Daniels often combined well, but without finding a final delivery that gave Callum Wilson or Yann Kermorgant an opportunity.
Four minutes after half-time, Kermorgant hooked Pugh’s cross over, before Kermogant slid the ball into Wilson inside six yards, only for Wilson to tread on the ball and fall over with the goal gaping.
Kermorgant and Wilson combined again on 54 minutes to play Wilson in behind the Rotherham defence, but with only Adam Collin to beat Wilson struck the outside of the post.
Six minutes later, Bournemouth’s goal finally arrived. Matt Richie picked out defender Cook at the back post with a delicate cross, and Cook, who had remained forward after a corner, duly nodded Bournemouth ahead.
At the other end, Alex Revell, Becchio’s replacement, failed to connect with a low delivery from Matt Derbyshire on the right after Kari Arnason had scooped a knock-down over the bar from a Taylor free kick shortly after.
Rotherham pushed forward searching for a leveller with 10 minutes remaining and Arnason again went close, curling an effort from outside the penalty area narrowly over, before Bowery struck in the final moments.