Manchester City midfielder Ilkay Gundogan also returns after missing two national team games in October with an injury.
Four-time world champions Germany now have a six-point lead in Group J after their win in Hamburg.
Toni Kroos played every minute at the 2014 World Cup when Germany won the title and had remained an important part of the team since.
Germany’s defenders — Mats Hummels in particular — will be wary of England forward Jadon Sancho, though he’s been given only six minutes of playing time by England coach Gareth Southgate.
'Rainbow armband symbol for diversity': UEFA stops investigation into Manuel Neuer's Pride Month gesture
Neuer has been sporting the rainbow-coloured armband to show support towards the LGBT+ community during 'Pride Month'.
Following their World Cup debacle three years ago, Germany has much to prove at the Euro 2020 finals, postponed from last year, after which Loew will step down after 15 years in charge.
Madrid said on May 17 that Kroos tested positive while already in isolation after contact with another person who recorded a positive test.
Germany's Nations League clash with the Netherlands on Saturday in Amsterdam will be Loew's 168th international since taking charge in 2006, but Ballack says his 12-year reign should already be over.