Dortmund coach Jurgen Klopp made 10 changes to the side which had beaten Real Madrid 4-1 in the Champions League last Wednesday, keeping only defender Mats Hummels in his starting XI on Saturday.
They were nevertheless too strong for Dusseldorf and cemented second place in the table, which they can clinch for certain next weekend.
"It has been said for weeks that there is only one club who can rotate and still win games," said Watzke.
"I'm very pleased that we have now done that successfully for a second time, just to show people that we also have players who can prove themselves in such a Bundesliga match.
"I am also very pleased that we got this result so that nobody can criticise us of playing only half-heartedly."
Nuri Sahin was one of the beneficiaries of the rotation, staking a claim for a place against his former club on Tuesday with a dream goal to set Dortmund on their way to victory.
He also set up the second for Jakub Blaszczykowski and praised the atmosphere within the club, in spite of the ongoing transfer speculation surrounding the likes of Hummels and Robert Lewandowski.
"It is no secret that we all have a very good relationship with each other," he said on his club's website.
"The lads here are simply sensational."