Lewandowski netted a brace in Bayern's 5-0 win and his double meant he has now recorded a goal against all 18 Bundesliga clubs.
Flick revealed how he had tried to inspire the striker, who moved onto 43 goals in all competitions this season.
"I told Robert Lewandowski that I was surprised to hear at the press conference that he had not yet scored a goal against Fortuna Dusseldorf and that he should change that as soon as possible," he said after the game.
"And of course he did."
Bayern's win saw it move 10 points clear at the top as it nears an eighth straight league title, and it has netted 86 goals in 29 Bundesliga games this season.
But Flick insisted the 100-goal milestone was not a priority, with Bayern having five matches to net 14 times.
"There are other goals that are more important to me. That we have a very successful season," he said.
"If this is the case, that we can score one or two goals more, that's even better.
"But currently the focus is on the Bundesliga. To finish the league on the same pitch as we are now."