A 2-1 loss at Greenhous Meadow saw 10-man Millers eliminated in the second round of the FA Cup by Shrewsbury.
Lewis Grabban's first-half penalty gave the Millers a hard-earned lead but Marcus Marshall's dismissal on the stroke of half-time left Rotherham with plenty of work to do in the second half.
Ian Sharps equalised soon after the interval and despite holding firm for most of the second period, Nicky Wroe's penalty seven minutes from time eventually proved the difference.
All three changes to the Millers' squad from last week's fixture against Crawley came to the defensive line.Marcus Marshall replaced Dale Tonge at right-back, Guy Branston stepped in for Jason Taylor and Tom Newey filled in for the ineligible Jon Harley.
Meanwhile former Millers man Sharps wore the captain's armband for the Shrews as they looked to continue their impressive form.
The Shrews were always likely to offer stern resistance on their own patch, as their last defeat at Greenhous Meadow came back in March.
The match began slowly on a cold and blustery afternoon in Shropshire and play was halted in the early stages for Branston to nurse a head injury.
The first chance for the Millers came on the 10-minute mark as Brett Williams bought a yard with excellent control from Sam Wood's header but Chris Neal was equal to his rasping effort.
Terry Gornell then fashioned a chance for the Shrews at the other end but Wood, back on defensive duty, got a critical touch to deny the hosts a chance to shoot.
Shrewsbury began to exert some pressure on the Millers and Lionel Ainsworth met a deep cross-field ball with a stinging volley that needed sharp reactions from Conrad Logan to keep the ball out at the near post.
A punted ball forward caused problems for the Millers' defence and the ball eventually fell to Marvin Morgan, but Mullins charged down the bustling striker's shot.
Alex Revell was keen to make it a difficult afternoon for the Shrews' rear-guard and a well-won header saw the ball break for his strike-partner Williams, but his left-footed strike ballooned over the crossbar.
Shrewsbury almost capitalised on a moment of hesitation when Gornell nipped in to pinch the ball deep in Millers territory.He fed the ball wide to Ainsworth and returned to the box to meet a delightful cross with a powerful header but a heroic save kept the game goalless.
Almost immediately the Millers broke down the other end and a dangerous ball in by Marshall squirmed through towards Wood who was fouled as he shaped to shoot.The referee had no hesitation in pointing to the spot and Grabban stepped up to net his 13th goal of the season.
However Rotherham were reduced to 10 men before the break.Marshall mistimed his tackle as pacey winger Mark Wright nipped past him and was dismissed for a second yellow card. Andy Scott withdrew Williams so that Tonge could slip into the vacant right-back position.
Half-time: Shrewsbury 0 Millers 1
Despite being at a numerical disadvantage the Millers almost extended their lead within a minute of the restart.Revell escaped the offside trap on the right-wing before delivering a low, measured cross but it just evaded the onrushing Wood.
Instead the game's second goal went the way of the home side.A left-wing corner bounced loose and appeared to hit a hand before Sharps stabbed the ball home.The referee waved away the protestations and allowed the goal to stand.
The Shrews looked keen to exploit their extra man and right-back James Hurst was allowed to gallop forward before released a low left-footed drive but it skidded fractionally wide of Logan's near post.
Rotherham were forced into their second substitution after Branston hobbled off on the hour mark to be replaced by Michael Raynes.
The hosts' forward partnership was linking up well and Gornell slipped a perfectly-weighted ball through to Morgan, but Logan had his angles covered and got a strong palm in the way to deny the striker.
Matt Richards was exploiting the extra space in the midfield and was first to react to a poor clearance but he dragged his shot just wide of the post from the edge of the box.
Rotherham were penned back and had to endure a succession of corners as Shrewsbury pressed.A left-footed shot by Morgan looped goalwards after a deflection but Logan again produced an incredible save to turn the ball over.
With the hosts controlling all the possession at Greenhous Meadow it looked increasingly like set-pieces would provide the only outlet for the Millers.They nearly did just that as Mullins applied the deftest of touches to Schofield's free-kick but it flicked just wide of the post with Neal rooted to the spot.
For all their resistance the Millers found themselves staring down the barrel when Morgan went to ground under a challenge by Mullins.Wroe lashed the resulting penalty into the net to give the Shrews the lead with just minutes remaining.
Chris Holroyd was introduced soon after in place of Mullins as Andy Scott threw all his attacking options onto the field to try and salvage a result.
However it proved futile as the hosts saw out their lead to have their name in the hat for the third round draw.
Full-time: Shrewsbury 2 Millers 1
Shrewsbury: Neal; Jacobson, Sharps, Cansdell-Sherriff, Wright, Wroe, Morgan, Richards, Ainsworth (Taylor 86), Gornell (Collins 77), Hurst.
Subs (not used): Smith, McAllister, Regan, Bradshaw, Goldson.
Goals: Sharps (48), Wroe (83 pen).
Millers: Logan; Marshall, Mullins (Holroyd 86), Branston (Raynes 60), Newey, Grabban, Harrison, Schofield, Wood, Williams (Tonge 45), Revell.
Subs (not used): Warrington, Warne, Foster, Taylor.
Goal: Grabban (42 pen).
Sent off: Marshall (45).
Attendance: 4,048 (317 away).
Report: Richard Dorman
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