The 23-year-old failed asylum seeker had lived in Germany for eight years.
His body was found in temporary accommodation on Tuesday, six days after being flown to Kabul.
Political opponents called for Mr Seehofer to resign, saying he was unsuitable for the job.
“Hopefully his laughter has stuck in his throat… it’s high time he goes,” said left-wing Linke MP Jan Korte.
Mr Seehofer said the man’s death was “deeply regrettable” but rejected calls to step down, saying the decision to deport him had been taken on a local level.
The unnamed man, originally from northern Afghanistan, had come to Germany as a minor. He had been living in Hamburg and had convictions for theft and resisting officers.
He was put on a flight on 4 July with 68 other failed asylum seekers, as part of a German programme to deport Afghans to areas of the country seen as safe. The policy is part of an EU-wide push to step up removal of failed asylum seekers.
He was given a temporary place to stay at a hotel run by the International Organization for Migration for returning migrants who have nowhere to go.
The 23-year-old is thought to have killed himself some time on Tuesday. The Pro Asyl charity said he had apparently been forced into a situation where he had no way out, and it warned there was a risk it might not be an isolated case.
Why did Seehofer joke about Afghan deportations?
Mr Seehofer made the comment as he was presenting his own “migration masterplan” on Tuesday.
Of the 69 migrants flown to Afghanistan, 51 had come from his home state of Bavaria, where he leads the centre-right Christian Social Union. According to official figures 148 Afghans have been deported this year.
“Of all things on my 69th birthday – and I didn’t order this – 69 people were sent back to Afghanistan,” Mr Seehofer remarked. “That’s way above the usual level so far.”
A controversial figure in the government, he sparked a row that threatened to bring Chancellor Angela Merkel down, by demanding tighter controls on the Bavarian border with Austria.
Gyde Jensen, chairman of the human rights committee in the German parliament, the Bundestag, said that judging from the cynicism of his remarks, Mr Seehofer was “obviously in the wrong post”.
Another opposition figure, Claudia Roth, called for further deportations to Afghanistan to be halted due to “the continuing disastrous security situation”.