The City trio all started for Portugal in Lisbon but France's N’Golo Kante struck the only goal of the game to secure a result which ensures it is the world champions and not the Iberian nation who will finish top of group A3 and so progress to the finals.
Meanwhile, Ilkay Gundogan enjoyed the Nations League bragging rights on City colleague Oleks Zinchenko as Germany overcame Ukraine 3-1 in the latest round of qualifiers.
Gundogan played the full 90 minutes in Leipzig while Zinchenko was replaced four minutes from time after earlier hitting the post.
Roman Yaremchuk had given Ukraine an early lead before former Citt winger Leroy Sane levelled affairs.
A brace from Chelsea striker Timo Werner then secured the win which leaves Germany needing just a point against Spain on Tuesday to top group A4.
Elsewhere, Ferran Torres played the full 90 minutes for Spain as Luis Enrique’s side drew 1-1 away to Switzerland.
Remo Freuler had given the Swiss a first half lead and Spain were grateful to Gerard Moreno for a late leveller after Sergio Ramos – on the night he won his 177th cap created a new European record for international appearances – had seen two penalties saved.
Eric Garcia and Rodri were both unused substitutes for Spain.