Vicky Pryce, 60, of Clapham, south London, denied the charge, claiming Huhne coerced her into taking the points.
The jury of eight women and four men was discharged at Southwark Crown Court in London after telling trial judge Mr Justice Sweeney it was "highly unlikely" that even a majority verdict would be reached.
Mr Justice Sweeney told the jury: "I have received your note which indicates that it is 'highly unlikely' that you are going to reach even a majority verdict.
"I am grateful for that.
"Against the background of the length of time that you have been in retirement already, I have decided therefore, and it is my decision one way or the other, that I must discharge you from any further deliberations.
"That means that your role in this case is now over."
Pryce, who will now face a retrial, showed little emotion as the judge discharged the jury, sitting with her chin in her hand.
A retrial is anticipated to start on Monday, the court heard, and Huhne, who has already pleaded guilty, will not be sentenced until after that retrial.
Pryce denies perverting the course of justice, claiming a defence of marital coercion, saying Huhne forced her to take the points.
The allegation dates back to 2003, when Huhne's BMW was clocked speeding on the way from Stansted Airport as the then-MEP travelled back from Strasbourg.
He already had nine points on his licence and risked being banned - which he feared would affect his chances of being nominated as the Lib Dem candidate for Eastleigh, Hampshire.
Pryce, who had a clean licence at the time, said he forced her to take the points, waving a pen at her in their hallway as he forced her to sign a form confirming she committed the offence.
The jury heard Pryce confided in her daughter Georgia Beesley at the time, saying Huhne had pestered her into taking the points.
He lost his licence anyway that year after being caught talking on his mobile phone while driving, the court heard, but went on to be nominated as the Lib Dem candidate for Eastleigh and won the seat in 2005.
The allegation about the speeding points became public in May 2011 when it was published in two Sunday newspapers - nearly a year after Huhne ended his 26-year marriage to Pryce, confessing to an affair with PR adviser Carina Trimingham.
During the trial, it emerged that Pryce - once a top economist for the Government - spent months trying to reveal the points-swapping to the press so she could "nail" Huhne, 58, after he left her for Ms Trimingham in June 2010.
She first approached the Mail on Sunday via a freelance journalist in late 2010, claiming Huhne had passed points to constituency aide Jo White.
But that later proved to be untrue, and the story did not run.
In March 2011 she told Sunday Times political editor Isabel Oakeshott about the points-swapping and in emails the women discussed Pryce's desire to "nail" her ex-husband.
The court also heard recordings of four calls between the former couple, as Pryce tried to catch him confessing.
The revelations that Huhne had passed points to someone ran in both newspapers on May 8 2011, and it quickly emerged that it was Pryce.
Police launched an investigation and Huhne and Pryce were charged with perverting the course of justice in February last year.
Huhne, then energy secretary, stepped down from the Cabinet, vowing to fight the charges.
His lawyers tried to get the case thrown out but when that failed, he changed his plea on the first day of trial and resigned as Eastleigh MP, ending his political career.
During Pryce's trial, the mother of five said her ex-husband put his political career first throughout their marriage, while she was forced to compromise her own successful career.
She revealed in court that Huhne demanded she have an abortion in 1990 because it would be bad for his career.
He tried the same thing two years later, the court heard, but she resisted, giving birth to their youngest child.
Huhne left Pryce in June 2010 after confessing to an 18-month affair with Ms Trimingham during half-time of a World Cup game when it was about to be exposed by a newspaper.
Pryce claimed she wanted to expose his wrongdoing by revealing the points offence, but had not wanted to ruin his career.
"If I really wanted to inflict fatal damage on him, I could have done something very, very different," she told the court.
Jurors heard glowing testimonials about the economist from several high-profile figures, including Sir John Scarlett, former head of MI6.