Southgate, 46, had been undefeated in four games as interim manager following Sam Allardyce's abrupt departure last year.
"I take a lot of encouragement from that despite the result," said Southgate. "It's never nice to lose, but I have to be pleased with the way the players played and how our tactical system worked."
Podolski's thunderbolt gives Germany 1-0 win over England
Southgate hailed Lukas Podolski's second-half thunderbolt goal on his final appearance for Germany, but noted that England outplayed the world champions for long spells.
"It was an incredible strike, and from [goalkeeper] Joe Hart's point of view, it was pretty unstoppable," admitted Southgate.
Gary Cahill captained England as part of back-three alongside Michael Keane, who was making his debut, and Chris Smalling.
We need to have Germany's winning mentality, says England manager
Southampton's James Ward-Prowse and Nathan Redmond also won their first England caps.
Adam Lallana hit the post and Dele Alli saw a shot blocked at point-blank range as England ruled the first half in a creative, threatening and energetic display.
"I thought we were the better side up until their winning goal, that was a good learning experience for our young players who made their debuts," said Southgate."All that was missing was the finish to get the winning goal which I felt we deserved."
Southgate saw plenty of plus points to take forward into Sunday's World Cup qualifier against Lithuania at Wembley.
"We walked through the three-man defence a few times and only had limited chances to prepare it," said Southgate. "Michael Keane had an excellent debut and the system is perfect for Lallana and Dele Alli.
"I have seen Germany pin teams back with the system we have played in the past, I didn't want us to be on the back foot and we created the better chances we had. It's a great option for us to have. We have to play specific systems for specific games, but we need to be flexible.
“I decided on the system six weeks ago after watching Germany. I was delighted with the way the team implemented it, but we won't necessarily do that for every game. It's very exciting for what we can do moving forward."
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