The 21-year-old was given permission on Friday to leave the Germany national team training camp and fly to London to put the finishing touches to his deal.
Germany head coach Joachim Low confirmed he would not return for the side's Nations League match against Switzerland on Sunday, making him available for Chelsea's opening Premier League fixture on Sept. 14.
"If he were to travel to Switzerland and return, I believe, he'd have to go into quarantine and the player, of course, wants a good start at Chelsea and this would be a disadvantage for him," Low said.
The medical is not expected to raise any issues and the Blues are set to confirm Havertz as a Chelsea player by the end of the week, taking their summer spending spree past £200m with the acquisitions of Hakim Ziyech, Timo Werner and Ben Chilwell in addition to free signings Thiago Silva and Malang Sarr.
Havertz was an unused substitute in Germany's 1-1 draw against Spain on Thursday evening. The decision not to play him was taken following consultation with Chelsea to avoid any risk of injury complicating his medical.