The Dutch defender made the £13m move to St Mary's from Scottish champions Celtic in September 2015, signing an initial five-year contract.
Van Dijk, 24, has now committed to the club until the summer of 2022.
"The club is growing and I definitely want to grow with them, that's how I feel," the Netherlands international told the club's official website.
Van Dijk, who made his Saints' debut in the goalless draw at West Brom on the opening day of the season, has played every minute of Southampton's Premier League campaign this season, forming an impressive centre-back partnership with Jose Fonte.
The Breda-born defender made his international debut in October 2015 in the Netherlands' 2-1 win over Kazakhstan in the Euro 2016 qualifiers.
Southampton director of football Les Reed says van Dijk will be a "key pillar" in Ronald Koeman's squad for many years to come.
"Although Virgil only joined us in September we felt it was important to strengthen our commitment and we believe this also provides further indication of how serious our ambitions are for the coming years," he said.
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Virgil van Dijk has signed a new six-year contract with Southampton, just eight months into his current deal.