The result puts them four clear of bottom-placed Falkirk and it means the Ayrshire side are just one point better off than their hosts.
Inverness boss Terry Butcher kept the faith with defender Lionel Djebi-Zadi, who was sent off in last week's Scottish Cup defeat by Falkirk, for the SPL visit of Kilmarnock, while striker Adam Rooney made a rare start.
Killie, who had lost three times to the Highlanders this season, were without Frazer Wright with a knee injury, with David Fernandez returned to the bench after his hamstring troubles.
With Falkirk and St Mirren out of action, the hosts were aiming to trim the gap on their visitors to a point ahead of next weekend's trip to bottom side Falkirk.
A lively start saw Inverness keeper Ryan Esson called into action after 50 seconds when he got down well to block from Craig Bryson.
Then Kevin Kyle fed the ball in for Danny Invincible, but the big forward failed to connect with it.
Moments later, Invincible hesitated when put clear again, allowing Ross Tokely to challenge and clear it.
On 18 minutes, Caley Thistle stole into the lead when Tokely's sweeping ball into the box was met by Richie Foran's header as he outjumped keeper Alan Combe on the six-yard box.
It was exactly the start the relegation-threatened team were looking for, just 10 days after their 1-0 win at Ibrox, which shot them off bottom spot.
And the advantage was doubled just three minutes later when Ian Black's free-kick, with the wind behind it, fooled everyone including Combe to finish in the bottom right corner.
The two-goal lead did not stop the Caley Jags from pressing forward as they sought another to kill Killie off, without carving open any clear opportunities.
The wind was whipping around the Tulloch Caledonian Stadium as Jim Jefferies' men probed for a goal before the interval.
And their efforts paid off when Garry Hay's cross was driven into the area and Simon Ford was on hand to head home, giving his side a lifeline.
Kilmarnock made a flying start to the second half and keeper Ryan Esson had to be lively to push away a Gavin Skelton effort in the opening seconds.
The visitors continued to push for the leveller, much to the frustration of Butcher on the sidelines.
Chances were few and far between, with the battle in the midfield rarely resulting in creating attacks.
With 15 minutes to go, Tokely tested Combe with a low drive, but Combe got down well to hold it.
Substitute David Fernandez cut the ball back into the box moments later, but Lionel Djebi-Zadi was there to swipe it clear.
Killie finished the stronger team, but Caley Thistle held on for a precious three points in their bid for top-flight survival.