Saints also rejected a bid from Liverpool for Fonte’s defensive partner Dejan Lovren on Friday as new boss Ronald Koeman attempts to end the summer exodus from St Mary’s.
Adam Lallana and Rickie Lambert have departed for Liverpool, and Manchester United have bought left-back Luke Shaw.
Saints - who also lost their coach Mauricio Pochettino to Tottenham - therefore have around £60 million in the bank and no need to sell any of their remaining stars.
Executive director Les Reed reiterating that stance following the £27million plus add-ons sale of Shaw.
"While we are sad to see Luke depart the club, we fought to ensure that we got the right deal for a player in whom we have invested a great deal of work over the past decade," he said.
"This deal is a good one for Southampton Football Club, and hopefully sends a clear message to other clubs wishing to bid for our players.
"Luke's transfer fee will be reinvested into the team as our new manager, Ronald Koeman, builds for the new season and for years to come."
Lovren and Fonte formed a fine partnership in the heart of the Saints defence last season.
Fonte joined the club from Crystal Palace in 2010 for a fee reportedly in the region of £800,000 and has since made 173 league and cup appearances for Saints.
He does though only have one year left on his contract so Southampton must decide whether to cash in now or risk losing him for nothing next summer.