Michael Smith’s first-half goal and David Ball’s late tap-in ensured the Millers made it 10 matches unbeaten.
Early pressure paid off after 14 minutes as Rotherham went ahead through Smith, who latched on to Joe Newell’s clever chip to poke past George Long.
The hosts held off a good spell from Wimbledon, which saw Lyle Taylor’s effort blocked, before the impressive Newell blasted over.
Matty Palmer should have marked his debut with a goal but he skewed wide an easy chance from Newell’s cross.
Wimbledon still threatened and it took a good tackle by Josh Emmanuel to deny Cody McDonald a sight of goal.
Rotherham pushed for a clincher and Jon Taylor tested Long after being set up by Ball and Newell poked wide.
Wimbledon almost got leveller late on but Harry Forrester could not connect cleanly with a volley.
Rotherham then secured the win in the second minute of added time as Ball followed in from Ryan Williams’ saved shot.