Huhne and ex-wife Vicky Pryce, who faces the same charge, will appear before Westminster Magistrates' Court on February 16 to answer allegations that he persuaded her to take his penalty points for a speeding offence in 2003.
The Liberal Democrat MP for Eastleigh in Hampshire declared he was innocent and would mount a "robust defence" against the charge, which carries a maximum sentence of life imprisonment.
His departure forced a mini-reshuffle which saw Lib Dem business minister Ed Davey promoted to the Cabinet as Energy Secretary. The vacancy left by Mr Davey in the Department for Business was filled by Norman Lamb, a parliamentary aide to Deputy Prime Minister Nick Clegg.
The changes - which involved only Lib Dem MPs - were announced by Mr Clegg, who said he was hoping Huhne would make a swift return to Government if he was acquitted.
In a letter to his former leadership rival, Mr Clegg said: "I fully understand your decision to stand down from Government in order to clear your name, but I hope you will be able to do so rapidly so that you can return to play a key role in Government as soon as possible."
However, the Prime Minister made no mention of a possible return in his own letter accepting Huhne's resignation, saying only: "Like the Deputy Prime Minister, I am sorry to see you leave the Government under these circumstances and wish you well for the future."
Huhne, 57, is the third Cabinet minister - and the second senior Lib Dem - to be forced out since the formation of the coalition in 2010, following David Laws and Liam Fox.
His departure will be rued by Lib Dems on the left of the party, who saw him as one of the ministers most able to stand up for their values against Conservatives in Cabinet.
Environmentalists voiced dismay at the loss of what Greenpeace described as "a vocal advocate for the green agenda in a Government whose green credentials are looking more than a little tarnished".
Announcing his resignation in a 30-second statement outside his London home, Huhne described the Crown Prosecution Service's decision to press charges as "deeply regrettable".
"I am innocent of these charges and I intend to fight this in the courts and I am confident that a jury will agree," he said.
"So as to avoid any distraction to either my official duties or my trial defence, I am standing down, resigning, as Energy and Climate Change Secretary. I will, of course, continue to serve my constituents in Eastleigh."
Pryce, a prominent economist, told the BBC she hoped for a "quick resolution" to the case.
The Prime Minister and Mr Clegg discussed how they would handle the fall-out from a possible charge in a phone conversation at 9am today, Downing Street said.
Ten minutes later, Mr Cameron was informed of the charge by his office as he travelled to RAF Northolt for a flight to the South West, 50 minutes ahead of the official announcement by Director of Public Prosecutions Keir Starmer at 10am.
The PM took a call at 10.40am from Huhne, who offered his resignation in a conversation lasting five or six minutes. Within 20 minutes, Mr Cameron had contacted Mr Davey to offer himHuhne's old job.
Speaking later during his visit to Plymouth, Mr Cameron said: "I think Chris Huhne has made the right decision, given the circumstances."
The events which led to today's charges date back almost a decade to March 2003, when Huhne's car was allegedly caught by a speed camera on the motorway between Stansted Airport in Essex and London.
Accusations of impropriety did not emerge until after the MP's 26-year marriage ended in 2010 as a result of his affair with PR adviser Carina Trimingham.
Pryce told the Sunday Times last year that her ex-husband - then an MEP - had asked "someone" to take the penalty on his behalf to avoid losing his driving licence.
Huhne and Pryce were interviewed by Essex Police detectives before the case was handed to the CPS, but a decision on possible prosecutions was delayed by a court battle to obtain key emails from the newspaper.
Announcing the charges in a televised statement, Mr Starmer said: "All the available evidence, including the new material, has now been carefully considered by the CPS and we have concluded that there is sufficient evidence to bring criminal charges against Mr Huhne and Ms Pryce for perverting the course of justice.
"The essence of the charges is that, between March and May 2003, Mr Huhne, having allegedly committed a speeding offence, falsely informed the investigating authorities that Ms Pryce had been the driver of the vehicle in question, and she falsely accepted that she was the driver.
"Accordingly, summonses against both Mr Huhne and Ms Pryce have been obtained from Westminster Magistrates' Court and those summonses will now be served on them. They are due to appear in court on February 16 this year."
Other Government changes resulting from the resignation saw Lib Dem MP for Cardiff Central Jenny Willott appointed an assistant Government whip and East Dunbartonshire MP Jo Swinson take Mr Lamb's old post as parliamentary private secretary to Mr Clegg.
Despite widespread speculation, there was no return for Mr Laws, who quit as Chief Secretary to the Treasury in May 2010 and was later suspended from the Commons for seven days after an expenses scandal.
PA
