Tottenham trio Dele Alli, Harry Kane and Harry Winks were forced out of the initial 25-man squad, with Raheem Sterling, Fabian Delph and Jordan Henderson later withdrawing.
Kane withdrew from the squad on Monday after taking a knock during Spurs' win over Crystal Palace last weekend, but questions were asked about the severity of his injury when Mauricio Pochettino said he would be fit for next weekend's north London derby against Arsenal.
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Speaking in a press conference, Southgate said: "We've had to change plans because there was so much uncertainty coming in but we've got the players we've got and I've really enjoyed the week.
"New players coming in - it's a great opportunity for us to look at them."
Asked if he was satisfied that all the players who had withdrawn were genuinely injured, Southgate said: "Yeah, absolutely.
"Harry Kane - I knew he was in trouble because he stayed down - Harry Kane doesn't stay down.
"Both him and Harry Winks were scanned, our medical department reviewed, and there is no way they're available for our two games. Spurs might risk them for the Arsenal game, that's a different matter.
"I hear this talk of club v country - it's nonsense. They are injured and they can't play."
In late March England played Germany in Dortmund, where that friendly match was marred by offensive chants about the World Wars from a section of visiting supporters.
Ahead of the latest meeting between the nations, Southgate condemned the rogue fans responsible for the songs and praised Germany for deciding to pay their own respects by wearing black armbands bearing poppies.
Of the chanting, the England boss said: "I think it's completely unacceptable. We have a huge percentage of fans who follow us away but there was an element shouting things that night that were unacceptable.
"We're talking about individuals and the vast majority of the supporters are brilliant.
"I think Germany have taken a huge step in terms of agreeing to wear the poppy."
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