Standard Sport reported in March that Chelsea have been keen on the Netherlands international for much of the season, though Liverpool and City had emerged as rivals in what would likely be a £50million transfer battle.
The 25-year-old, signed from Celtic for £13m in 2015, has been sidelined since an ankle injury ended his season in January, and Puel is adamant his defensive linchpin has not played his last game in a Saints shirt.
“It was a bad injury for him and for us,” said Puel.
“Then after Jose Fonte left (for West Ham) it was difficult for us. It’s been a good thing to see Jack Stephens and Maya Yoshida play together in their place. But for Virgil it was a bad injury.
“Now the surgery is finished he can work normally and be ready for next season – with us.
“He’s our captain and I have said he is important for us. He has authority, the leadership of the team, he is a fantastic player.
“It’s important for us, of course, to wait until the beginning of the season to see him on the pitch with Southampton.
“He has a long contract and the directors want to keep him.”