The midfielder struck twice in as many minutes just before the hour and a drilled finish late on earned him the match ball - and his side a 24-point advantage over second-placed Aberdeen.
Celtic enjoyed some early pressure on a difficult pitch, with Anthony Stokes having a close-range effort chalked off for offside, but Kilmarnock slowly established a foothold - without ever troubling Fraser Forster.
Kris Boyd had a penalty claim rejected by referee Willie Collum as Efe Ambrose appeared to give him a nudge in the box.
Commons and Leigh Griffiths worked Kilmarnock goalkeeper Craig Samson as Celtic continued to forage for the opening goal.
But the visiting fans had to wait until the 56th minute for the breakthrough as Commons worked a neat one-two with Griffiths before scoring with a flick of his left boot.
Two minutes later he raced onto Adam Matthews' low cross to give Samson no chance and thereafter it was all about whether the Celtic man could claim his second hat-trick of the season.
He warmed Samson's gloves from 12 yards, saw another attempt disallowed before his low drive from 22 yards (86) found the bottom corner.
The result leaves Celtic seven ponts from their 45th Scottish title and the spectre of a relegation play-off still hanging over Kilmarnock, who are just four points off 11th-placed Ross County.