The 90th-minute dismissal of substitute Mitchell Rose for a foul on Aaron Dawson was the only negative for them.
Captain Ian Sharps was the match-winner with a 42nd-minute headed goal and the centre-back then marshalled his defence in the second half in atrocious conditions at St James’ Park.
Victory delighted Millers chief Steve Evans, who said: “The roller-coaster continues.
“I said earlier we have had the good, we have had the bad but we haven’t had the ugly yet.
“The ugly is when you win after not playing particularly well, but it was a big win against a good team that we respect.
“Exeter have beaten Bradford away, which is tough, and gone to the league leaders and thoroughly deserved to win.
“The only disappointing thing from my point of view is that we weren’t two or three up at the interval as you always know that you are going to have some late pressure from Exeter, but we did well.
“We said to the players in the team talk that we would settle for a thoroughly professional 1-0 victory, where we worked really hard and had a disciplined shape.
“People will think that we plucked that shape from nowhere, but we picked that shape with the personnel we had in mind.”
Evans was full of praise for his back five and especially the performances of Sharps, the returning Johnny Mullins and goalkeeper Andy Warrington as they leapfrogged their hosts, who are now ninth.
Exeter City: Krysiak, Tully (Dawson 89), Bennett, Baldwin, Coles, Sercombe, Oakley, Doherty (Keohane 30) O’Flynn 59), Gow, Cureton, Moore-Taylor. Unused substitutes: Evans, Amankwaah, Chamberlain, Reid.
Rotherham United: Warrington, Bradley, Sharps, Mullins, Ridehalgh, Pringle, Taylor, Cameron (O’Connell 90), O’Connor, Nardiello (Rose 86), Revell. Unused substitutes: Thompson, Odejayi, Hunt, Rooney, Walker. Sent Off: Rose (90).
Referee: O Langford (W Midlands).
Man of the match: Ian Sharps.