Caley Thistle seemed destined to suffer a familiar hard-luck story after Dean Shiels netted an early opener in a rare moment of class from the home side at Rugby Park on Saturday, but Shinnie levelled before the break and completed a four-goal spree from the visitors in 13 second-half minutes.
Jonny Hayes had put Inverness in front with a brilliant strike in his first start since his previous trip to Ayrshire resulted in a shoulder injury during a Scottish Communities League Cup defeat at Somerset Park in August.
Gregory Tade twice finished well as Inverness repeatedly exposed a disorganised defensive display from the hosts, who pulled goals back through Shiels and Paul Heffernan.
Inverness manager Terry Butcher has consistently stated their overall displays have deserved more this season and everything clicked into place today as his team refused to buckle after the early setback.
David Davis gave Caley Thistle's front players the platform to perform with a powerful display in central midfield and advanced midfielder Shinnie shone above everyone with a busy and inventive performance capped with some superb finishing.
The only disappointment for the visitors was that Dunfermline's win at Easter Road kept them bottom, but that will hardly matter.
Kilmarnock were unchanged for the fifth consecutive game after going four matches unbeaten but they were slow from the start.
Anssi Jaakkola beat away a swerving effort from Davis before Shinnie got in behind left-back Rory McKeown but trundled an effort wide from outside the box.
Kilmarnock took the lead in the 13th minute after Heffernan backheeled the ball into the path of Shiels, who had time and space to pick his spot.
Jaakkola made decent saves from Greg Tansey, Shinnie and Hayes before the match briefly turned ugly when Davis stopped Killie taking a quick free-kick. The resulting confrontation prompted both of Bobby Madden's assistants to run towards the centre-circle to help restore calm before the referee booked Davis, Shiels, Tade and Mohamadou Sissoko.
The hosts were struggling to get out of their own half and Inverness grabbed a deserved equaliser in the 39th minute after a short corner.
Hayes returned a pass to Shinnie to put him in behind his marker in the left channel and the former Rangers youngster advanced before guiding the ball just inside the far post from a tight angle.
Only Jaakkola's smart double save in injury-time from Hayes and Tade prevented Kilmarnock going into half-time behind but the pattern of play did not change and Inverness took the lead in the 53rd minute.
Hayes was allowed to turn and run at the home defence and the Irishman took full advantage by drilling a left-footed shot into the bottom corner from 25 yards.
Jaakkola parried a curling effort from Meekings before Kilmarnock manager Kenny Shiels made a bold double switch in the 59th minute, bringing on wide men David Silva and James Dayton for James Fowler and Liam Kelly.
But the hosts fell further behind within a minute. Killie right-back Alex Pursehouse played an inside pass straight to Shinnie and he stroked the ball into the top corner from 22 yards.
It was 4-1 two minutes later. A Kilmarnock attack was cleared towards Tade just inside his own half but he was able to run away from the home defence before rounding Jaakkola and slotting home.
Killie were being run ragged and Davis slipped Tade clean through again but he pulled his shot wide of the far post.
Tade appeared to be brought down in the box by Pursehouse but Madden waved play on and the reprieve proved temporary as Shinnie completed his hat-trick.
Davis beat two men to race through the heart of the home defence and Shinnie took over as his team-mate stumbled, confidently finding the bottom corner.
Shiels netted from the penalty spot in the 73rd minute after Kenny Gillet had brought down Dayton but Inverness continued to dominate.
Tade completed the rout in the 83rd minute with his left foot after a simple reverse pass from Shinnie left him in yards of space on the edge of the box.
Heffernan got another consolation in the closing seconds with Ryan Esson unable to keep out his low shot.