Havertz stroked home from the spot early in the second half in Dortmund following a handball by Joachim Andersen, the unlucky Danish defender who had a goal disallowed at the other end only moments earlier.
Musiala, of Bayern Munich, then ran away to stroke in the second goal midway through the second half as Germany’s class told.
At one point it looked as if the game could be abandoned as English referee Michael Oliver stopped play in the 35th minute of the first half and took the teams off the pitch while a violent storm passed overhead.
Torrential rain, hailstones, high winds, thunder and lightning caused a break in play of 25 minutes before the action could resume.
It made for a memorable night, and one that ended with the host nation coming through a stern test of their credentials to keep alive their dream of winning the trophy in Berlin on July 14.
The path is set to get much tougher from here, however, and Julian Nagelsmann’s team will now go to Stuttgart for a quarter-final next Friday against either much-fancied Spain or surprise package Georgia.
Meanwhile Denmark, who famously beat Germany in the 1992 European Championship final, go home without winning a game — they had qualified from their group with three draws.
Nagelsmann made three changes to the Germany side following their last outing, a 1-1 draw with Switzerland.
Nico Schlotterbeck replaced the suspended Jonathan Tah in central defence, David Raum came in at left-back, and Leroy Sane was preferred to Florian Wirtz on the right wing.
Schlotterbeck, of Borussia Dortmund, thought he had given Germany the lead inside four minutes when he headed in a corner in front of the enormous South Stand.
He ran off in celebration, but the goal was disallowed due to a foul by Joshua Kimmich.
It threatened to become a frustrating night for the home team as they were then thwarted on several occasions by Danish goalkeeper Kasper Schmeichel.
He tipped over a rasping drive by Kimmich and turned a Havertz volley around the post as the Danes weathered the early storm.
Another one was coming, and when the action eventually restarted with the pitch now sodden, Germany quickly cranked up the pressure again.
A Raum cross from the left was met by the head of Havertz, but Schmeichel –- whose father played in that 1992 final — was once again on hand to make a good save.
The Danes did pose a threat on the break as they attacked towards their own supporters, but Rasmus Hojlund hit the side-netting after catching Schlotterbeck in possession, and then saw Manuel Neuer come out and save at his feet.
The game was interrupted again for the half-time break, before Denmark –- and Andersen in particular — were left to rue two VAR interventions at the beginning of the second half.
First, on 48 minutes, Andersen thought he had scored when he fired in as the ball broke to him in the box, but the VAR team told the referee to rule out the goal because of an offside against Thomas Delaney, who had provided the assist.
As soon as play resumed, Germany attacked and a Raum cross deflected off the outstretched hand of Andersen in the area.
The Crystal Palace player’s offence was penalised following another check, and Havertz scored his second penalty of the competition.
Havertz and Sane missed great chances to make it 2-0 before Musiala latched onto a simple ball over the top and ran through to net his third goal of the Euros to become the joint-top scorer alongside Georgia’s Georges Mikautadze.
Wirtz, on from the bench, had a late goal that would have made it 3-0 disallowed for offside, but Germany have momentum and will take some stopping now.
AFP
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