Rotherham were riding a six-game unbeaten run and buoyed by a 4-0 win at Oxford in midweek.
Dagenham beat Rotherham 5-0 earlier in the season and took the lead just shy of the hour mark when Medy Elito scored a penalty after Kari Arnason fouled Elito.
Arnason was dismissed for the foul.
But Rotherham were on terms three minutes later when central defender Claude Davis headed home.
However, the 10 men of the Millers could not find a winner and they conceded again on 82 minutes when Luke Wilkinson scored the winner for Dagenham.
Rotherham drop back to sixth with the defeat, two points adrift of the top three.
Steve Evans said: “We’ve done more then enough to win three games today.
“But you only win games if you put the ball in the net and it’s hard to take.
“They’ve nicked a win - that’s the bottom line - that’s what they’ve done. They’ll never nick three points like that again.”