Paul Warne's Millers initially fell behind at home to Fleetwood Town, but recovered to take a 2-1 lead into the interval.
The second 45 did however belong to the visitors, who struck three times without reply to win Saturday's contest by a 4-2 scoreline.
“I didn’t think we were at our best today, for whatever reason. Our press wasn’t athletic enough and I felt like we didn’t move the ball quick enough," Warne told Rotherham's official website.
“I wasn’t pleased at half-time and I told the lads at half time that I didn’t think they were playing at their best.
“The lads have been excellent so far, but today was our worst performance of the season.
“I think in terms of chances, we created enough to win the game, sometimes you can play poorly and win but it wasn’t to be."
Callum Morton's 24th-minute effort handed Fleetwood the ascendancy against the run of play, though Rotherham got back on terms seven minutes before the break, Michael Smith guiding a header from Wes Harding's long throw-in into the bottom corner.
Callum Camps then pulled Chiedozie Ogbene back inside the box, presenting Kieran Sadler with an opportunity which he duly took to United in front from the penalty spot deep in stoppage-time.
Three goals in the space of 15 second-half minutes from Gerard Garner, Danny Andrew and Camps would however prove more than sufficient for the Cod Army to leave South Yorkshire with all three points.
Defeat leaves the Millers 13th in the League One standings.
Meanwhile, Doncaster drew first blood at Wigan Athletic, Tommy Rowe firing home on 22 minutes after Joe Dodoo's hooked ball into the Latics' box was allowed to bounce not once, but twice.
But, the hosts were level just moments later when Will Keane found the net, and the same player slotted beyond Pontus Dahlberg to decide the contest eight minutes after the break.
Saturday's result means that winless Rovers have now lost five out of six in the league this term, and sit bottom of the pile with just a single point to their name.