The Scottish defender poked home from close range after Leeds failed to clear a Paul McLaren free-kick.
Leeds had dominated the first half with Clarke Carlisle hitting the woodwork three times in the first eight minutes.
Michael Ricketts wasted another chance after the break and, after McIntosh pounced, Mike Pollitt produced two good saves late on to ensure victory.
Leeds boss Kevin Blackwell:
"We should have had it done and dusted inside the first 10 minutes. "We dominated from start to finish. If that had been in the real world, then they'd have been reported for mugging as we looked the good side.
"Fair play to Rotherham. They came at us in the second half. We needed some luck but we created our own problems."
Rotherham: Pollitt, Stockdale, Swailes, McIntosh, Hurst, Campbell-Ryce (Mullin 86), Barker, McLaren, Proctor, Butler, Junior. Subs Not Used: Montgomery, Scott, Vernazza, Monkhouse.
Booked: Barker.
Goals: McIntosh 77.
Leeds: Sullivan, Kelly, Carlisle (Richardson 13), Butler, Kilgallon, Wright, Gregan, Oster (Lennon 70), Walton (Joachim 81), Healy, Ricketts. Subs Not Used: Carson, Spring.
Att: 8,860.
Ref: P Crossley (Kent).
MMIX
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