Junker pounced on a mistake by Germany keeper Tim Wiese to equalise after the visitors had led for most of the game.
Striker Mario Gomez had fired them into the lead in the 19th minute and substitute Patrick Helmes added a second in the 72nd after a trademark quick break.
Danish striker Dennis Rommedahl crowned his 100th international appearance with a goal two minutes later to cut the deficit.
"This is the first time this team played together so I think they did well," said Germany coach Joachim Low. "This is not a tournament and we are still in preparation."
Second-string Germany, with only one starting World Cup player in their line-up, were initially put under pressure with the Danes missing clear chances through Daniel Agger and talented teenager Christian Eriksen.
Despite Germany's absences following their third place finish at the World Cup last month, Low stuck to his favoured 4-2-3-1 system with Gomez as the lone striker.
This was a rare start for the 25-year-old following a disappointing first season at Bayern Munich and a goalless World Cup.
Gomez repaid Low's trust in the 19th minute when he was picked out by stand-in captain Thomas Hitzlsperger with a beautiful through ball and slotted home his 13th goal in 39 games.
"Ja Mario," shouted Low from the bench, with the coach looking for options in attack for the Euro qualifiers against Belgium and Azerbaijan next month.
Denmark squandered a great opportunity to level in the 56th minute when Eriksen curled a free-kick into the box, keeper Wiese cleared but Agger managed to hit the post from four metres.
Helmes completed a swift counter attack in the 72nd minute, seemingly sealing their win but Rommedahl pulled one back with a well-struck left-footed shot.
The Danes then took advantage of the Germans' lapse of concentration, with Junker beating the offside trap and punishing Wiese's bad clearance at the edge of the box.
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