Mercedes have been utterly dominant throughout the 2019 F1 season, winning nine of the opening 10 Grands Prix.
But the tricky conditions at Hockenheim completely caught Mercedes out as one driver crashed out and another nursed their car home in 11th as Max Verstappen took the chequered flag for Red Bull.
Hamilton looked to be cruising in the wet conditions, but as the track dried and other teams began changing their strategy throughout the race, the tide quickly turned against him.
Charles Leclerc crashed out on the final corner, and Hamilton followed him a lap later, only to save his car from the gravel trap before crawling back to the pits with a broken front wing.
He ended up finishing third from last after making a number of pit stops with his championship lead in serious jeopardy from Bottas.
But the Finnish driver failed to take advantage as he spun out before crashing into the barriers to end his race.
The German Grand Prix marked a milestone achievement as Mercedes marked their 200th Grand Prix as their team members sported retro 1950s-inspired outfits.
The cars were also given a new makeover to celebrate 125 years of Mercedes-Benz in motorsport, veering away from the traditional all-silver look to bring in some white to the front of the vehicles.
But Wolff believes there was some karma from the changes Mercedes made aesthetically which cost them on Sunday.
“It shows that you cannot fool around with staff – you should concentrate on the job,” he said.
“We’re not superstitious but we believe in karma, and this is a day to learn.”
Hamilton caused pandemonium in the pits when he crawled in for a new front wing as his crew weren’t ready for him.
“It was unfortunate because he crashed right at the entry of the box of the pit lane and you’re not prepared and we made the wrong calls afterwards,” Wolff added.
And Bottas’ mistake meant Mercedes missed out on scoring any points in a race for the first time since the Austrian Grand Prix last year.
“Many others made the mistake, Leclerc crashed, but overall for us it was a bad day for the drivers. Simply, it cannot have gone much worse,” the Mercedes boss said.
Mercedes still hold a huge advantage over their rivals in the constructor standings, but that hasn’t eased the pain for Wolff from this weekend.
“It doesn’t make it any easier when you have a day like this,” he said.
“We had a decent start to the race, with good pace but then obviously you add incidents, cars crashing out in tricky conditions, making the wrong calls, and this is where it can all start to go wrong.”