Having brought on Naismith for skipper David Weir, Rangers began the second half in determined style.
"We felt it at Rangers when he left here, " said Naismith of his former team-mate.
Scotland forward Steven Naismith denied any suggestions of unrest among the players over Levein's formation.
Steven Naismith, Calum Elliot and Zander Diamond all went close for Scotland in the first-half.
BBC: SPORT | Football | Internationals | Slovenia U21 1-0 Scotland U21
Leon Osman and Steven Naismith were on the score sheet to stun Brendan Rogers' men.
Naismith has now won six Bank of Scotland SPL awards and has scored 18 goals this season.
BBC: SPORT | Football | My Club | Kilmarnock | Naismith unsure of his next move
Steven Naismith skilfully worked his way down the left wing and cut the ball infield to Miller.
Kilmarnock's Naismith drilled in a 10-yard strike moments later but Slovenian keeper Samir Handanovic was able to clear.
BBC: SPORT | Football | Internationals | Slovenia U21 1-0 Scotland U21
But Killie manager Jim Jefferies insists that it is not in preparation for the sale of Steven Naismith.
Naismith then had a go at the other end but he blasted well over and Ma-Kalambay was never troubled.
BBC: SPORT | Football | Scottish Cups | Rangers 1-0 Hibernian
Naismith squandered another chance when through on goal, failing to find enough contact when found by a Davis chip.
Rangers improved after the interval and Maurice Edu had shot saved, while a Steven Naismith header hit the bar.
Ten minutes later, Ferguson's corner found Naismith unmarked in the box and he spun and volleyed home from close-range.
And Smith was happy to see both Naismith and Cousin on the scoresheet.
"We are hoping to keep Steven Naismith and nothing has changed, " said Jefferies.
Killie almost made it 3-0 when Wales nodded Garry Hay's free-kick back across goal and Naismith headed against the crossbar.
Naismith thought the Scots still had a chance of qualifying for the finals in Poland and Ukraine despite the defeat.
Cousin responded by netting the opener before Steven Naismith, Chris Burke and Kris Boyd helped themselves to a goal apiece.
McCulloch and Ferguson then saw efforts cleared off the line before Naismith's close-range header cracked off the underside of the crossbar.
BBC: SPORT | Football | Scottish Cups | Rangers 1-0 Hibernian
And the visitors took the lead when Invincibile finished beautifully after being fed by Naismith, who had burst forward from midfield.
Walkit, a U.K. walk-routing website, adjusts for hills using Naismith's Rule, developed by William W. Naismith, a Scottish mountaineer, in 1892.
Naismith came on for Edu and quickly got on the scoresheet when he converted David Weir's cross with a well-placed header.
Steven Naismith had already squandered a good opportunity before Edu rose above goalkeeper Cesar Sanchez to head home with 34 minutes gone.
Rangers and Scotland forward Steven Naismith took a different view, saying Ferguson's continued absence from the Scotland squad is a "massive loss".
Naismith, 20, picked up the same award from the Scottish Football Writers last year and was thrilled to complete a personal double.
BBC: SPORT | Football | Scottish Premier | Nakamura takes top player award
Rangers' Steven Naismith was inches away from scoring an own goal when his clearance crept across the face of goal and out.
Midfielder Maurice Edu, who had earlier hit the post, side-footed the winner, completing a fine move involving Steven Naismith and Kenny Miller.
But the visitors rarely threatened in the second half and Miller, Steven Naismith and Gregg Wylde came close to adding to Rangers' tally.
However, Celtic were denied a cleansweep when Aiden McGeady was beaten to the Young Player of the Year by Kilmarnock striker Steven Naismith.
BBC: SPORT | Football | Scottish Premier | Nakamura takes top player award
In fact, Rangers hammered four past Well in 20 minutes, with Steven Davis, Kenny Miller and Vladimir Weiss adding to Steven Naismith's strike.
BBC: Rangers boss Walter Smith forgives initial sluggishness
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