The Foreign Office confirmed that Sir Ivan had not sought any further civil service job.
Sir Ivan shocked Westminster and Brussels with his resignation as permanent representative on 3 January and used an email to staff to criticise “muddled thinking” over Brexit.
A Foreign Office spokeswoman said: “Sir Ivan Rogers resigned as UK permanent representative to Brussels on 3 January.
“He did not seek any further civil service appointment and has therefore resigned from the civil service with immediate effect.
“We are grateful for Sir Ivan’s work in Brussels and across a number of other senior positions in the civil service.”
It is understood Sir Ivan will receive three months’ pay in lieu of notice, in line with standard Foreign Office terms, but no special “payoff” was offered or sought.
He is being succeeded by career diplomat Sir Tim Barrow, a former ambassador to Russia described by No 10 as a “seasoned and tough negotiator” who will help the government make a success of Brexit.
In a fiery message to staff announcing his resignation from the Brussels post, Sir Ivan hit out at the “ill-founded arguments and muddled thinking” of politicians and said civil servants still did not know the government’s plans for Brexit.
The news of Sir Ivan’s departure from the civil service came as a leading businessman and Tory donor warned about the dangers of leaving the single market.
Sir Andrew Cook, who has given a reported £1.2 million to the Conservatives, said he would find it impossible to continue to fund the party if Theresa May’s Brexit plans involved quitting the single market.
He warned that jobs and exports depended on membership.
Sir Andrew, the chairman of William Cook, a firm producing components for rail, energy and defence uses, highlighted how much his company relied on exports to mainland Europe and the supply of skilled labour from the continent.
He told BBC Radio 4’s Today programme: “There are barriers to entry without the single market, there are tariffs. There is a desire by my competitors in mainland Europe to exclude me from the market. Were it not for the single market I would not be trading with these people.”