Lincoln City 2 Wigan Athletic 1
Boosted by the Scottish star's return to the side after seven matches out with injury, Latics gave as good as they got for the opening 45 minutes against the promotion chasers.
Curtis Tilt had a shot blocked and Chris Merrie fired over for Latics, with Brennan Johnson and James Jones shooting just wide at the other end.
Latics were rewarded for an enterprising start to the second period when Naismith put them ahead on 53 minutes with a right-foot shot that took a deflection on its way in.
The lead lasted only 16 minutes, however, with Lincoln making the most of a hugely-contentious free-kick award on the edge of the area, Jorge Grant curling the set-piece beyond the clutches of Jamie Jones.
From then on it was virtual one-way traffic, and Latics dodged a bullet when a mistake from Naismith - who nodded the ball back into the danger zone from the dead-ball line - presented the ball to Joe Walsh, whose header was cleared off the line by Tom James.
But the respite was only temporary, and Tom Hopper's snapshot from close range with seven minutes remaining was past Jones before he could react.