It took a second-half stunner from Lukas Podolski in his final international appearance for Germany to settle Wednesday's friendly fixture in Dortmund.
England, however, performed better and were unfortunate not to spoil the party at Signal Iduna Park as they were made to pay for their missed chances with Adam Lallana hitting the post and Dele Alli wasting a one-on-one situation.
"I'm very pleased with what we learned, the manner of the performance. The one bit we missed was the finish. We should have had the game won, really," Southgate said.
"I'm very pleased with the performance, lots of excellent individual performances. Most pleasing of all is the new tactical system we tried, the players carried it out very well and it suited the players we had.
"It suited the opposition we were playing against. We don't like losing, but in games like this it is important to learn something, and to try things, and I think we've done that, and I want the players to build on what they've done."
Southgate deployed an experimental 3-4-3 formation and the visitors looked comfortable in Germany as centre-back Michael Keane made his full senior debut, while James Ward-Prowse and Nathan Redmond made appearances off the bench.
Asked about the system, Southgate said: "I'm sure we will [use it again], it's a great option for us to have, I think a lot of the players are playing it at their club, which helps.
"We've also got some intelligent footballers in there, and it's pleasing for me, because I think we needed that ability, and we showed it.
"It's great for the two young ones at the end to get a feel of international football. Really pleased with Michael Keane, I think he had an excellent debut and can be very proud of that; he used the ball very well, defended well, and throughout the team there were some good performances. We've lost to a fairy-tale goal."