The Gers fought back from a losing position to claim victory for the sixth time this season in the league, and went four points clear as a result ahead of Celtic's clash with Dundee United at Parkhead later in the day.
Scotland striker Miller converted twice from the penalty spot before grabbing the winner, with Connor Sammon netting a brace for an impressive Killie side, who had Mohamadou Sissoko sent off in the 54th minute for conceding both spot-kicks.
Miller now has 18 SPL goals so far this season.
Rangers made two changes from the side who defeated Aberdeen. Madjid Bougherra was out with a hamstring injury, while Vladimir Weiss dropped to the bench. Kyle Lafferty and Richard Foster were both drafted into the team. Kilmarnock were unchanged.
The home side could have opened the scoring after just two minutes when Alexei Eremenko released Sammon into the box and he found himself with only Allan McGregor to beat but the goalkeeper raced off his line and did well to block.
Killie still looked dangerous and a thunderous shot from Eremenko was forced out of play by an alert McGregor. The breakthrough came after 21 minutes when Eremenko's chip found Liam Kelly at the back post and he cut back for Sammon to bundle home from close range.
Kilmarnock pushed forward in search of a second goal and Mehdi Taouil was allowed to surge unchallenged into the box only to see his poor effort comfortably smothered by McGregor.
Rangers were back on level terms when referee Euan Norris pointed to the penalty spot after 41 minutes for a Sissoko trip on Miller.
The striker brushed himself off to take the spot-kick himself and confidently dispatched into the back of the net from 12 yards, after seeing his penalty saved last week.
Despite the setback of losing a goal late in the first half, Kilmarnock looked lively when they emerged for the restart and were quickly causing more problems for their visitors.
Craig Bryson tried to set up Sammon inside the six-yard box but the effort caught under the body of McGregor and Foster reacted first to hook to safety off the line as the goalkeeper tried to recover.
But the Rugby Park side were left reeling when they conceded a second penalty after 54 minutes, this time for a Sissoko foul on Lafferty. The Killie player picked up a second yellow card before Miller lashed high into the net from the spot once again to hand Rangers the advantage.
The striker then spurned a great opportunity to claim his hat-trick when his shot fizzed across the face of goal and wide with the gaping net at his mercy.
The Ibrox side were left rueing that miss when Kilmarnock equalised after 59 minutes. Jamie Hamill whipped a great ball from the right into the box where Sammon was waiting at the back post to rifle home and claim a double.
But, in another twist, Rangers restored their lead just four minutes later when Miller had the net bulging again, this time from open play when he collected a Steven Whittaker cross in plenty of space and rifled past goalkeeper Cammy Bell.
Rangers were under pressure when Killie won a free-kick 25 yards out with five minutes remaining but were able to breathe a sigh of relief when Hamill screwed just wide of target.
Miller then had the opportunity to put the game beyond their hosts for Rangers when he bore down on goal only to see his point-blank effort blocked by Bell.
In the end, the Scottish champions were able to hold on for the win, and put some pressure on rivals Celtic, despite the best efforts of Kilmarnock.