The verdict was delivered on Friday after a 15-week trial, but Black, who will appeal, will not be sentenced until November 30.
He was acquitted of nine other charges, including racketeering and failing to file corporate tax returns.
Black and his fellow defendants were accused by US prosecutors of stealing $60m in payments that should have benefited Hollinger International, of which he was chairman.
Black and three former associates were found guilty of illegally taking a total of $6.1m in payments from Hollinger International.
They took 'non-compete payments' from two subsidiaries of Hollinger, in an agreement to not compete with the subsidiary if they left the company. One subsidiary, American Publishing Company, owned a small newspaper in California which it was in the process of selling.
The conviction for obstruction of justice covered Black's removal of evidence from his Toronto office, a scene captured on security cameras.
Hollinger shareholders pushed Black out of the company in 2003, along with chief executive David Radler, who went on to testify as a key witness for the prosecution after pleading guilty to one count of fraud.
The Canadian-born tycoon was once worth £400m and headed a media empire which included the Telegraph, The Jerusalem Post and The Chicago Sun-Times. He and his wife Barbara Amiel were well-known for throwing lavish parties attended by the cream of society.
His legal fees are believed to run to millions of pounds and he is facing civil lawsuits from the US Securities and Exchange Commission, as well as the Sun-Times Media Group, as Hollinger is now known.