Sanches, 18 at the time, became a key player after he was given a starting place from the quarter-final onwards, while Guinea Bissau-born Eder scored the winning goal in the final against France after he was brought on as a substitute.
However, Eder has struggled for form at Ligue 1 side Lille this season and Sanches has had difficulty settling in at Bayern Munich after a 35 million euro (£30.32 million) move from Benfica, making 17 league appearances with only five starts.
The pair were left out of the squad for a friendly against Cyprus and World Cup qualifier away to Latvia next month.
Coach Fernando Santos said the same squad would also travel to the Confederations Cup in Russia "unless there are extraordinary situations.
"They are players who were European champions and gave everything and brought great happiness to the Portuguese people," coach Fernando Santos told reporters.
"These moments are uncomfortable but I have to talk to players and make choices. It's part of life and I don't have a problem with it. (And) who was it who picked Eder when nobody believed in him? Last year, in this same room, I was asked why I had selected him. Now, it's the other way around."
(Writing by Brian Homewood; editing by Mark Heinrich)
