The comprehensive victory has seen Germany move onto six points in Group C, three points clear of Italy Under-21s ahead of their meeting in Tychy on Saturday night.
Germany were unchanged from their 2-0 victory over Czech Republic Under-21s last time out, meaning that Serge Gnabry and Mitchell Weiser continued in the final third alongside Davie Selke, while Maximilian Arnold captained the team once again.
Denmark boss Niels Frederiksen, however, made three changes from the 2-0 defeat to Italy Under-21s, with Jacob Rasmussen, Frederik Borsting and Lucas Andersen making way for Jakob Blabjerg, Casper Nielsen and Mikkel Duelund.
Toljan was again the provider in the 11th minute as the right-back found Weiser with a smart cross from a wide position, but the attacker turned his effort just wide as Denmark survived another dangerous moment.
All of the opportunities were coming for Germany, with excellent work from Gnabry handing Max Meyer a brilliant chance to register in the 23rd minute, but the Schalke 04 midfielder fired over the crossbar from close range.
Czech Republic's first opportunity of the match arrived just past the 30-minute mark when Andrew Hjulsager used his blistering pace to break into a shooting position, but the number seven could not find a route past Germany goalkeeper Julian Pollersbeck, who made a smart save.
It was Germany that finished the first period on the front foot - coming close to opening the scoring through Selke, Meyer and Gnabry - but the two teams headed down the tunnel on level terms.
A thunderous strike from Mahmoud Dahoud came close to sending Germany ahead minutes into the second period, but Denmark goalkeeper Hojbjerg was on hand to make the stop once again.
The pressure was relentless, however, and Germany finally made the breakthrough in the 53rd minute when Selke curled an unstoppable effort into the top corner from the edge of the Denmark box.
Cardiff City's Kenneth Zohore came off the Denmark bench just before the hour as Frederiksen's side looked to respond, and the forward brought a smart save from Pollersbeck in the 58th minute after placing a free kick towards the bottom corner.
Zohore had another opportunity for Denmark 20 minutes from time, but once again he found Pollersbeck in smart form as the Germany goalkeeper kept his side ahead with a flying save.
Denmark's response to conceding the first goal was impressive, but the match was taken away from them in the 73rd minute when centre-back Marc-Oliver Kempf found the back of the net with a spectacular volley from inside the box.
Two then became three in the 79th minute when substitute Nadiem Amiri danced into the Denmark box before finding the back of the net with a straightforward finish.
Germany will book their spot in the semi-finals of the competition as Group C winners if they avoid defeat against Italy on Saturday night.