He won a soft free-kick on the edge of the area after a challenge from Gary Mason, but he dusted himself down to curl the ball past Mark Howard.
It was another late win for the champions on an afternoon where they huffed and puffed for much of the 90 minutes.
Celtic made their intentions clear from the outset and won two corners inside the opening minute to put Saints under early pressure.
But the home side handled it well and hit back with both Will Haining and Andy Dorman coming close with shots from outside the area which slipped just wide.
St Mirren coped comfortably with anything Celtic could muster in the opening half-hour and goalkeeper Howard was untroubled.
Aiden McGeady should have done better on a Celtic counter-attack with St Mirren short at the back, but he dragged his shot carelessly across goal when he had time and space to do better.
It took a great tackle from Massimo Donati to keep out Craig Dargo as St Mirren showed they could also pose a threat.
However, chances were few and far between at either end in a poor first half.
McGeady forced a great save from Howard nine minutes from the break with a low shot which the goalkeeper turned for a corner.
But Saints broke clear from the flag-kick and it took the save of the half from Artur Boruc to prevent David van Zanten opening the scoring.
Celtic lost skipper Stephen McManus through injury early in the second half with Darren O'Dea coming on to replace him.
Georgios Samaras almost broke the deadlock after 55 minutes but dragged his shot narrowly wide with St Mirren on the back foot.
The right boot of Boruc saved Celtic five minutes later when Billy Mehmet struck a fierce shot which was bound for the net until the goalkeeper reacted.
If anything, St Mirren looked the more likely to break the deadlock as Celtic struggled to put together any cohesive play.
Nakamura was sent on by Bhoys boss Gordon Strachan to try and change things as his team looked to be running short on ideas and it proved a significant substitution.
It worked as Celtic began to take a firmer grip on midfield and pushed St Mirren deeper and deeper into their own half.
There reward came after Eddie Smith penalised Mason and Nakamura conjured up his moment of magic with just three minutes left.