Roy Hodgson's men were undone by Per Mertesacker's first-half header as they recorded the country's first back-to-back home defeats since 1977.
"It's obviously disappointing - you never like to lose at Wembley and it's normally a good game against the Germans," Jagielka told the FA's official website. "It's not very nice to lose [but] there will be a lot of positives to take out of it. I think, in the first half, we played some good football and were unfortunate to go in 1-0 down.
"[In the] second half we were looking for the goal to get back in the game and they hit us quite frequently on the counterattack. There will be bits and bobs to look at but, on the whole, it was nice to have two friendly games over this period rather than any qualifiers."
The two matches saw vastly differing lineups as Hodgson experimented, including the likes of debutants Adam Lallana, Fraser Forster and Jay Rodriguez - a development Jagielka welcomed.
"I think it's important that the manager does give people the opportunity to play," the Everton man continued. "When we meet up again [in March] we'll be that much closer to Brazil and the manager may not want to tinker with it as much.
"We'll take the positives that we will be in Brazil. The preparation will start after Christmas. The confidence has taken a bit of a dent but, to the same extent, we've got quite a few months until the next meet up. There wasn't going to be too much momentum taken over to the games that will be played before Rio, so we'll have to dust ourselves off and get back on the horse for the friendlies coming up before the World Cup."