Miller struck twice from close range in the second half after Boro skipper Mark Roberts nodded the visitors level, cancelling out Neill Collins' header. Chris Porter completed the scoring, getting ahead of his marker to score with another header.
Both sides started well, with Michael Doyle shooting over the crossbar from the edge of the area and home goalkeeper George Long producing a good save to keep out Filipe Morais' header.
Collins opened the scoring after 19 minutes, heading in at the far post from Doyle's left-wing cross. But Stevenage equalised in the last minute of the first half when Morais' corner was met by the head of Roberts.
Kevin McDonald and Ryan Flynn combined to set up Miller after 55 minutes before he grabbed his second goal with another close-range finish after the Boro backline failed to clear Flynn's cross.
Visiting keeper Steve Arnold turned over a shot from Nick Blackman before Porter rounded off the scoring in the 87th minute, getting ahead of his marker to beat Arnold with another header.