The 33-year-old played the full 90 minutes of Oranje's 4-0 thrashing of Hungary over the weekend, which confirmed their spot in the quarter-finals as League A Group 3 runners-up.
Van Dijk was expected to be rested for Tuesday's finale with Bosnia-Herzegovina, as Netherlands boss Ronald Koeman is likely to rotate heavily with second place in the section already wrapped up.
However, the former Southampton and Celtic man has now left the national team camp ahead of the showdown with the Golden Lilies, as has Barcelona midfielder Frenkie de Jong, with both departing "on medical grounds" according to Koeman.
"For both Frenkie and Virgil it is better for them to leave the training camp at this moment. That decision was taken on medical grounds, with of course the interest of the players coming first," the Oranje head coach told the media.
Liverpool to assess Van Dijk before Southampton clash
Following confirmation from the Netherlands that Van Dijk had travelled back to Anfield early, Liverpool released their own statement, announcing that the defender would be assessed before the weekend's Premier League clash with Southampton.
"Liverpool captain Virgil van Dijk will not be involved in the Netherlands' second fixture of this international window on Tuesday night," the Reds said on their official website.
"He will return to the AXA Training Centre this week for assessment ahead of the Reds' campaign resuming with a trip to Southampton on Sunday."
It is unclear if Van Dijk is carrying a specific injury, but there has been no mention of an issue for the 33-year-old, who is expected to be fine for the clash with the Saints at St Mary's on November 24.
Van Dijk has played every minute for Arne Slot's side in the Premier League and Champions League this season, scoring two goals and providing one assist across those 15 appearances.
Will any injured Liverpool players return against Southampton?
With nothing on the line for the Netherlands and Liverpool about to hit a hectic run of festive fixtures, it makes sense for the national team to let Van Dijk head back to Merseyside prematurely, and Reds fans will no doubt be grateful for the decision.
The centre-back should shake off whatever affliction he is nursing in time for the weekend, but Trent Alexander-Arnold is more of a doubt with the hamstring injury he picked up against Aston Villa two weekends ago.
The right-back's problem forced him to withdraw from the England squad, but he is believed to have avoided a serious problem and should be in with a good chance of facing reported admirers Real Madrid in the Champions League on November 27.
Foot victim Harvey Elliott has also returned to full training two months after his fracture, but Diogo Jota, Alisson Becker and Federico Chiesa are seemingly fighting uphill battles to make the cut this weekend.
Liverpool hold a five-point lead over Manchester City at the top of the Premier League rankings, having accrued 28 points from their first 33 on offer in the 2024-25 campaign.