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The Germans face Gareth Southgate’s England at Wembley on Friday before hosting France four days later in Cologne in friendlies designed to test the defending champions before next year’s World Cup in Russia.
The burly Wagner, who has scored five goals for Germany in five appearances, drilled home a penalty on 56 minutes, then netted a header from a cross by ex-Leicester City player Andrej Kramaric on 80 minutes.
Hoffenheim had taken the lead after just nine minutes when midfielder Dennis Geiger stabbed the ball home at the second attempt.
The result lifts Hoffenheim to fifth, seven points behind leaders Bayern Munich who are now four-points clear at the top after Saturday’s 3-1 win at Borussia Dortmund, who drop to third.
Cologne remain rooted to the bottom, eight points from safety after 11 games with pressure growing on Austrian coach Peter Stoeger.
Wagner’s double in Cologne is well timed after Germany’s first-choice striker Timo Werner underlined his form after a neck injury with a goal and assist in RB Leipzig’s 2-1 comeback win at home to Hanover 96.
The 21-year-old Werner, who has featured eight times for Germany and scored six goals, played his first 90 minutes since September.
He set up Yussuf Poulsen’s equaliser, then netted an 85th-minute winner after the Brazilian Jonathas gave Hanover the lead at Leipzig’s Red Bull Arena.
The result left Leipzig second in the table, four points behind Bayern.
Later on Sunday, Wolfsburg were denied their first win since August in a topsy-turvy 3-3 draw at home to Hertha Berlin in a first-half dominated by the video assistant referee.
Striker Vedad Ibisevic put Hertha ahead after just 20 seconds before the VAR disallowed two Wolfsburg goals.
The hosts looked to have levelled with six minutes gone when defender Robin Knoche slid the ball over the goal-line, but the VAR saw an offside in the build-up.
With twenty minutes gone, Wolfsburg’s Germany striker Mario Gomez crashed a penalty across the crossbar.
Yunus Malli then slammed home a right-footed goal six minutes later for Wolfsburg, who were again denied a goal as the VAR spotted another offside.
However, Malli was not to be denied.
His header on 41 minutes stood before Gomez added a second on 44 minutes when his shot went in, having hit both posts, to put Wolfsburg 2-1 up at the break.
Hertha levelled at 2-2 when Dutch defender Karim Rekik headed home from a free-kick on 53 minutes.
Moments later Divock Origi, on loan from Liverpool, made it 3-2 for Wolfsburg when the ball hit his stomach and went into the goal.
Ex-Leipzig striker Davie Selke came off Hertha’s bench to score at the second attempt to equalise on 83 minutes.
The result leaves both teams in mid-table with Wolfsburg having drawn their last seven league games in a row.
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