Italian veteran Bonucci put Union ahead from the penalty spot in a dramatic first half, but Dortmund battled back to claim their fifth win of the season.
“We were really good today. I usually like to be critical, but I think we can be really proud of this performance,” said Dortmund defender Mats Hummels.
Last season’s surprise package Union have now lost their last seven matches in all competitions as they also struggle with the step up to Champions League football in this campaign.
“It is really tough mentally to have to take so many hits. I think the international break will do us good,” Union defender Robin Gosens told Sky.
Union started brightly but allowed Niclas Fuellkrug to give Dortmund the lead from a corner on seven minutes.
Fuellkrug’s joy was short-lived, however. Just two minutes later, he deflected a Gosens header into his own net to make it 1-1.
The drama continued with three game-changing VAR decisions in the space of 10 minutes.
Union’s Alex Kral and Dortmund’s Fuellkrug both had headed goals ruled out for offside before Hummels conceded a penalty with a late challenge on Sheraldo Becker.
Bonucci converted with ease to put Union in front and net his first Bundesliga goal, but Dortmund struck back with two goals in quick succession just after half-time.
First, Former Union player Nico Schlotterbeck whipped a breathtaking shot into the top corner from the edge of the area to level the score.
Minutes later, substitute Julian Brandt put the home side back in front as Dortmund tore through Union on the counter-attack.
The hosts sealed victory through another former Union player in the 72nd minute when Julian Ryerson’s long-range shot was deflected in to make it 4-2.
The win put Dortmund second overnight, while Stuttgart went top with a brilliant 3-1 win over Wolfsburg.
In-form Guinea striker Serhou Guirassy continued his brilliant run of form with a hattrick as Stuttgart came from behind to grab their sixth win of the season.
Yannick Gerhardt put Wolfsburg in front with a cool finish midway through the first half.
However, Guirassy converted a cool penalty in the second half before adding two more in the last 15 minutes to claim his second hattrick of the season.
The Guinea international now has 13 goals from his first seven matches, a new Bundesliga record at this stage of the season.
“It’s unbelievable. It’s such a pleasure to play here with these fans. I love Stuttgart, it’s a really nice city and we have everything we need for a great season,” said the striker.
There was stoppage-time drama in Saturday’s late match as Hoffenheim survived a late scare to win 3-2 at Werder Bremen.
After Bremen’s Romano Schmid cancelled out Maximilian Beier’s early opener, Grischa Proemel restored Hoffenheim’s lead on 29 minutes with a well-placed shot from the edge of the area.
It remained 2-1 until the 91st minute, when Jens Stage levelled the score with a brilliant half-volley.
Moments later, Marius Buelter immediately curled a low shot in off the post at the other end to cut the home side’s celebrations short.
Elsewhere, RB Leipzig were left frustrated after a wasteful performance saw them draw 0-0 at home to Bochum.
Bochum goalkeeper Manuel Riemann saved two penalties either side of half-time, denying both Xavi Simons and Emil Forsberg the chance to give Leipzig the lead.
Promoted side Darmstadt scored twice in the second half to clinch a 2-1 win away to Augsburg.
Tim Skarke’s screamer and Tobias Kempe’s penalty put Darmstadt ahead, and Ermedin Demirovic’s late strike for Augsburg was not enough to deny the visitors a second win in two weeks.