The trio were all named to start for Roy Hodgson's Three Lions side at the Olympiastadion, with Lallana taking up a role on the right of a three behind lone striker Harry Kane whilst Henderson featured alongside Eric Dier in a two-man central midfield and Clyne played on the right side of a back-four.
For their opponents, Can made just his fourth cap for his country - starting in an unusual right-back role for Joachim Löw's side, although all of his international appearances thus far have come in that position.
Although Hodgson's side performed well, it was Germany who boasted the advantage at half-time courtesy of Toni Kroos' strike from distance, which injured Stoke City goalkeeper Jack Butland could not keep out.
Mario Gomez's second-half header seemed to put the game beyond the visitors, but Henderson helped kickstart a spirited comeback as Germany failed to clear from one of his corner-kick deliveries and Tottenham Hotspur's Harry Kane spun towards goal and fired an excellent strike into the bottom corner.
After Lallana was replaced, substitute Jamie Vardy came on to score his first international goal to make it 2-2 by flicking past Manuel Neuer at his near post from none other than Clyne's cross.
And at the very death, another Spurs player - this time Eric Dier - powered an emphatic stoppage-time header home from Henderson's corner to secure a morale-boosting 3-2 win.
James Milner and Daniel Sturridge were both unused substitutes but are expected to feature in England's second friendly of a double-header when they take on Netherlands at Wembley Stadium on Tuesday night.
Sturridge, in particular, will be keen to take the chance afforded to him after both Vardy and Kane - two guarantees to be called up to the European Championships in France in the summer - both scored in the German capital.
Reds elsewhere all in action for their countries
Can's Die Mannschaft meanwhile face Italy in Munich, with Joe Allen and Danny Ward facing Ukraine for Wales a night earlier. Simon Mignolet's Belgium travel to Portugal on Tuesday night, although the Reds' first-choice goalkeeper is unlikely to play over No.1 Thibaut Courtois.
Elsewhere on Saturday, Dejan Lovren was an unused substitute for Croatia's 1-1 draw away at Adam Bogdan's Hungary after playing the full 90 minutes of a 2-0 win over Israel three days earlier. Bogdan came off the bench at half-time and did not concede in the 45 minutes he played.
Mamadou Sakho could be involved for France as they take on Russia on Tuesday, having missed out on his country's 3-2 win away at Netherlands on Friday - sitting on the bench throughout.
Philippe Coutinho, who played in his Brazil team's 2-2 draw with Luis Suarez's Uruguay in a 2018 World Cup qualifier on Saturday, sees his side take on Paraguay in another qualifier on Wednesday night and could feature after only playing 20 minutes of the previous game.
Elsewhere, Marko Grujić received his maiden senior call-up for Serbia alongside Lazar Marković - currently out on loan at Fenerbahce - but did not feature in their loss to Poland, whilst the latter wasn't in the squad presumedly due to a knock. However, they also face Estonia on Tuesday night and could play some minutes then.
Brad Smith played the full 90 of Australia's 7-0 thrashing of Tajikistan earlier this week and could also play against Jordan before the end of the international break.
Divock Origi, Christian Benteke and Roberto Firmino all pulled out of duty for Belgium and Brazil respectively with injuries and have stayed on or returned to Merseyside for treatment with the club.