The expulsions, the first of sitting or former Tory MPs, follow the public support both men gave to the breakaway Pro-European Conservative Party during the European elections in June.
Sir Julian, former MP for Aldershot, is now poised to join the Liberal Democrats to give Charles Kennedy his first high-profile defection. Mr Rathbone, former MP for Lewes and a former arts and health minister under Margaret Thatcher, may follow suit.
"It seems I have been savaged by a pack of the party's golden retrievers," said Sir Julian. "I am heartbroken only because I will not be allowed to go to the Tory party conference. I shall miss it."
Sir Julian and Mr Rathbone received warning letters from the party chairman, Michael Ancram, after they wrote to a national newspaper during the European elections saying they would "find it very difficult to know how to cast our vote".
Others who signed the letter include the former government whip Sir Robert Hicks and Sir David Knox, a former Tory vice-chairman. But the biggest scalp for Eurosceptics would be Lord Gilmour, the former defence secretary and lord privy seal, who described Mr Hague's position on Europe as "indefensible".
The expulsions are likely to outrage pro-European Tories and may threaten the uneasy truce in the party ranks.