The 18-year-old is set to move to the south coast in a deal worth around £10million, and talkSPORT understands the Premier League champions have insisted on a significant buyback clause.
Reports suggested earlier in the summer that Leeds United were also keen on a move, however it's the Saints who have won the race to sign the promising starlet.
A holding midfielder by trade, young Belgian Lavia is highly-rated at the Etihad Stadium and someone the club expects to enjoy a successful career at the highest level - hence the buyback clause.
Lavia made his City debut in last season's Carabao Cup clash against Wycombe Wanderers, before also appearing in the FA Cup.
With just two senior appearances to his name, Southampton will be hoping to get the midfielder up to speed quickly, however he will have a former teammate to keep him company at St Mary's.
Goalkeeper Gavin Bazunu has also made the journey from Manchester to Southampton after completing a move that could be worth up to £15m.
While City were reluctant to lose Lavia, the deal to bring in Kalvin Phillips has eased any concerns about squad depth in the centre of midfield.
That £45m deal - an initial £42m with £3m in add-ons - has been described as 'bonkers' by Darren Bent, who believes the champions have got themselves a bargain.
Speaking on talkSPORT Drive, Bent said: "For Kalvin Phillips it's fantastic being a part of arguably the best team around in Manchester City. He's a top player.
"I get it, they've always had two holding midfielders. Rodri's emergence into a top, top holding midfield player and Fernandinho leaving means that they need someone else there.
"For Kalvin Phillips, and his international aspirations given how key he was for England's success in getting to the final of the Euros, if he starts playing for this Man City team he could become a mainstay in the England team.
"But £42m for Kalvin Phillips? It's bonkers.
"When I heard this rumour a couple of months back, I was hearing fees like £75m, £80m and fees like that, but if they can get a player of that quality for £42m, wow.
He added: "I can't believe the fee.
"In today's market where people are splashing the cash left, right and centre, £50m here and £70m there - £42m for an England international!"