Kyle Walker and Andros Townsend have been called up to the England squad after John Stones pulled out through injury.
Stones missed the last two Everton games after suffering a knee injury in their Capital One Cup win over Reading on September 22.
Roy Hodgson named Stones in his squad for the upcoming Euro 2016 qualifiers against Estonia and Lithuania when it was announced last week, but on Tuesday night the Football Association confirmed the 21-year-old had withdrawn.
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"Everton defender John Stones, who missed the Merseyside derby at Goodison Park on Sunday, has been ruled out due to injury," an FA statement read.
The FA confirmed Tottenham duo Walker and Townsend had been called up as a result.
Walker has not played for England since the 1-1 draw in Italy in March, while Townsend last featured in the victory over Slovenia four months ago.
The FA also confirmed captain Wayne Rooney, first-time call-up Danny Ings and Swansea midfielder Jonjo Shelvey did not train at St George's Park on Tuesday.
"They will be monitored ahead of Friday's meeting with the Estonians," the FA said.
More than 75,000 fans are expected to attend Friday's game - the last qualifier at Wembley.
Hodgson's men will then fly to Vilnius to take on Lithuania three days later.
England have already qualified for the tournament in France after winning all eight of their matches so far.