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Despite helping Dortmund to a 5-1 rout of Wolfsburg, Hummels was booed and whistled by a section of home fans in their 81,359 sell-out stadium each time he touched the ball on Saturday.
The 27-year-old told Dortmund last Thursday that he wants to leave at the end of the season, with a year left on his contract, to join Bayern, who he left for Borussia in 2008.
Bayern's chairman Karl-Heinz Rummenigge wants to agree a price with Dortmund for Hummels before the clubs meet in the German Cup final on May 21.
But Dortmund's fans made their feelings known as they face up to the reality of losing a third star to Bayern in three years.
World Cup winner Mario Goetze left for Bayern in 2013 to be followed by star striker Robert Lewandowski a year later.
Several signs at Dortmund's Signal Iduna Park stadium during the Wolfsburg match simply read "Why?" -- directed at Hummels.
One huge banner on the stadium's packed south terrace read "The captain is the first to go overboard - best to do it immediately!" and the loudest jeers came from that area.
Hummels brushed off the whistles in post-match interviews, but his face told a different picture during the game.
"I want to make it clear it wasn't 80,000, more like 8,000 or probably even less," he said.
"I saw where they (the whistles) came from."
Hummels received some solidarity from his Dortmund team-mates.
"It wasn't easy to hear for the whole team, and must have certainly been harder for him," said Borussia defender Marcel Schmelzer.
"Mats deserves praise for handling it well."
Micky Beisenherz, a columnist for current affairs magazine Stern and a Dortmund fan, wrote: "Dear Mats, you weren't really surprised by the mass tinnitus (whistling) from the south stand, were you?
"Real disappointed love", he added, referring to the club motto "Echt Liebe" (Real Love).
Dortmund's bosses have defended Hummels' want-away wish.
"It was only a few of the fans who did that. I found it shameful and hope it won't be repeated," said Dortmund's director of sport Michael Zorc.
"We have a basic rule at Borussia Dortmund that no player in our jersey should be insulted or whistled."
But Hummels can expect a similar reaction from Dortmund fans for their last two league matches at Eintracht Frankfurt and home to Cologne, plus the cup final against Bayern on May 21.
Bayern's ex-president Uli Hoeness did not help matters on Friday when he said it was Hummels who had approached the Bavarians, something Bayern then denied on Saturday.
"On Friday there was oil thrown on the fire from Munich," said Zorc in the wake of Hoeness' claims.
"I don't know what was behind it, but you can come to some conclusions."
To compound Hummels' situation, the German media has dragged up his comments from 2013, in reaction to Goetze's departure, implying it was motivated only by money.
"Everyone has seen how good our team is, I just think that there is little reason to leave us from a sporting perspective," Hummels said three years ago.
But news of Hummels possible arrival at Bayern has not gone down entirely well in Munich either.
Morocco captain Mehdi Benatia, also a centre-back, has threatened to leave should Hummels arrive and rejoin Roma.
Bayern paid Dortmund 37 million euros (US$42.63m) for Goetze three years ago, while Lewandowski left on a free transfer.
Dortmund chief executive officer Hans-Joachim Watzke has said Bayern will have to "dig deep in their pockets" to meet the undisclosed asking price.
Hummels has a market worth of 38 million euros.
"Either they pay the asking price or forget about it," said Watzke.