The party failed to win a number of key seats, with Scottish president Sir Malcolm Rifkind unable to take the Edinburgh Pentlands seat from Labour's Lynda Clark.
Scots Tory chairman Raymond Robertson also failed to stage a reversal of the 1997 general election by defeating Jim Murphy in Eastwood.
And Phil Gallie could not topple Labour's Sandra Osborne in Ayr.
However, there was some joy for the party when Peter Duncan overturned a Scottish National Party majority in Galloway and Upper Nithsdale.
Elizabeth Smith came close in Perth - but lost out to the Scottish National Party by less than 50 votes.
The Scottish Socialist Party compounded the party's misery when it beat the Tories into fifth in Glasgow Maryhill.
Sir Malcolm managed to reduce the Labour majority but Pentlands was one of a number of seats seen as symbols of a Tory return after their wipe-out in the 1997 general election in Scotland.
Scottish Tory Leader David McLetchie took some comfort from the Galloway gain, despite a 2% fall in his party's share of the vote with 70 seats declared.
" It's very disappointing but we are not going to come to any snap decisions tonight "
That left the party in fourth place behind the Lib Dems for the first time, with the remaining results to come in two long-standing Liberal Democrat seats.
Mr McLetchie said: "The Tories are still an effective force in Scottish politics. One is better than nothing, we have broken the duck."
The Eastwood constituency was also a key target for the Conservatives who lost it in 1997 when Mr Murphy won with a majority of 3,236.
Eastwood had been the safest Conservative seat in Scotland until 1997 but the Labour landslide delivered it to Mr Murphy with a swing of 14%.
Mr Murphy enjoyed a comfortable win and a majority which increased from 3,236 to 9,141.
Mr Robertson came second with 13,895 votes and in third place was Liberal Democrat Allan Steele with 6,239 votes.
The Scottish National Party's Stewart Maxwell was fourth with 4,137 votes with the Scottish Socialist Party's Peter Murray on 814 votes and Independent Dr Manar Tayan on 247. Mr Robertson said he was "disappointed" with the result.
He told BBC Scotland: "It's very disappointing but we are not going to come to any snap decisions tonight."
He said the Conservatives needed to continue to work to rebuild trust among the electorate in the party.
Labour also held onto Ayr, which was won during the landslide of 1997.
However, Mrs Osborne's majority was cut from 6,543 to 2,545.
She won 16,801 votes with Mr Gallie in second place with 14,256 votes.
A recount was required in Perth before Annabelle Ewing held onto the seat for the SNP - by just 48 votes.
Ms Ewing polled 11,237 votes compared with 11,189 for the Conservative candidate in a seat which Roseanna Cunningham first won from the Tories in a 1995 by-election.
The Tories also suffered a blow when the Scottish Socialist Party eclipsed them into fifth place in the Glasgow Maryhill constituency.
Labour's Ann McKechin held the seat with a 44.5% share of the vote, with Liberal Democrat Stuart Callison in second place and the SNP's Alex Dingwall third.
But the surprise was that Socialist Gordon Scott pushed the Tories' Gawain Towler into bottom spot.
The SSP had announced during the campaign that its ambition was to establish itself as the fifth party in Scotland.