With St Johnstone beating Motherwell, Terry Butcher's side needed a victory to earn a place in the Europa League qualifiers.
But Andre Hainault's sweetly struck volley just before half-time was enough to secure Ross County's first SPL derby win at Victoria Park.
For Inverness it was a cruel end to their most successful season, which also saw them lose a Scottish Communities League Cup semi-final penalty shootout to Hearts.
Butcher's side had not been out of the Clydesdale Bank Premier League top three since November and had the chance to seal a European spot last weekend but blew a one-goal lead at home to Dundee United.
They had not lost in five games against the Dingwall side this season but they were second best after struggling to cope without several midfielders.
With Richie Foran and Ross Draper suspended, Inverness started with a four-man midfield with an average age of 20.
County created their first chance on 20 minutes when Ivan Sproule got in front of a defender to meet Evangelos Oikonomou's low cross but his first-time effort just cleared the top corner.
Mihael Kovacevic then powered his way to the 18-yard box and dug out a low shot that Antonio Reguero saved before Steffen Wohlfarth volleyed wide with the Spaniard scrambling.
The hosts broke the deadlock when Paul Lawson crossed for Canadian international Hainault to unleash a powerful volley that flew into the top corner from 10 yards.
Inverness almost lost another before the break when Josh Meekings hesitated inside the box under pressure from Sproule but Mark Fotheringham could not get hold of his shot and Reguero saved.
After the break Inverness found more urgency to their play with Billy McKay coming close when he flicked David Raven's shot just wide but they could not keep the pressure up and Lawson twice threatened from long range.
Raven had a half chance but Gallacher got down well to hold at the second attempt and the away fans were already resigned to defeat before Iain Vigurs hit Reguero's post with an injury-time free-kick.