The former left back, who made 371 appearances for the team, has brought a civil claim for more than £50,000 relating to the lease of his Chilworth mansion.
Saints rented the house for nine months, so that chairman Nicola Cortese and his family could live there after his appointment.
Mr Benali and his wife, Karen, who is also listed as a claimant, allege that the club breached the lease agreement by failing to make certain payments and by not maintaining the property to an adequate standard.
Saints stated earlier this month that they plan to “rigorously defend” the allegations. They made the announcement after responding to claims made by Saints legend Matt Le Tissier.
Mr Le Tissier alleged that his former teammate is banned from the football club, which he described as “nothing short of disgusting”.
A club statement said: “Mr Le Tissier refers to his friend Francis Benali having the best interests of the club at heart, while neglecting to mention that the same person is currently suing Southampton Football Club in relation to a lease dispute and lost ambassadorial fees.
“It is a legal action the club will be defending rigorously in the best interests of the club and its reputation.”
A date for a county court hearing is not yet set, but a window has been provisionally created for it in May.
The claim relates to Mr Benali renting out his £1.8m home, shortly after Markus Liebherr’s takeover of the club in 2009.
The house, a five-bedroom property situated on more than three acres, boasts an indoor pool, stables and a paddock.
It was leased by the club from October 2009 until July 2010.
Mr Benali alleges that Saints failed to pay thousands of pounds worth of rent during that time, and that the property was not kept up to standard, requiring repairs running into tens of thousands of pounds.
Papers lodged with the courts also say that, as part of the lease agreement – for which the club was reportedly charged less than the going rate – Mr Benali negotiated a matchday ambassador role at St Mary’s for himself, for which he would receive a minimum of £1,000 a month.
The 44-year-old claims that he was stopped from conducting those duties on a number of occasions and that Saints owe him £8,000 in unpaid fees.
The court papers say that, around August 2009, Mr Benali was introduced to Mr Cortese, who was looking for a property for himself and his family.
Mr Benali alleges that a deal was verbally agreed with Mr Cortese to let his home, which estate agents Savills had indicated had a rental value of £6,000 per month.
It is said that the initial arrangement was for Saints to pay £4,000 each month, with Mr Cortese personally adding £1,000. Additionally, it is claimed that an agreement was reached that would see the club employ Mr Benali as a matchday ambassador, paying him £500 per match, with a minimum total of £1,000 per month. The lease began in October 2009, but it is alleged that in December of that year Saints breached the contract by paying only £3,500.
Additionally, Mr Benali claims that Saints denied him access to perform his ambassadorial role for the home league matches against Tranmere and Exeter that month and, therefore, neglected to pay him £1,000.
In January 2010, it is said that a new agreement was reached, in writing, where Saints would pay £5,000 per month in rent, freeing Mr Cortese from his personal obligation of £1,000.
Mr Benali alleges that, in June 2010, the club was again in breach of the lease, paying only £1,000.
He also claims that he was again prevented from performing his ambassadorial duties once in January, once in February, and then for the whole months of March, April, May and June, amounting to a further £7,000 in unpaid fees.
It is claimed that damage was also caused to the kitchen hob, that the club neglected to have the windows cleaned, that they had failed to pay the TV licence fee and charges for Sky television for the month of June 2010, that the swimming pool was not cleaned as agreed and that the garden was not kept up to condition.
The claim says that the cost of making good dilapidations to the house came to £33,346, while the cost of making good damage to personal property (“chattels”) was £3,163.98.
The Benalis’ house was sold in September last year for £1.86m.
Mr Cortese and his wife, Alexandra, have since moved into a different property in the same area. That was bought in September 2010 for £1.785m and is registered in their names.
Saints did not respond to a request for comment.
Mr Benali said: “This has been an ongoing matter for some time, and is in the hands of my solicitors.”
More Saints stories