"It's incredible you've done this", Stallone said to Trump, adding that Johnson was the inspiration for the character Apollo Creed in his Rocky movies.
That led to Johnson being convicted by an all-white jury in May 1913 and getting sentenced to one year and one day in jail.
He married a white woman, Etta Terry Duryea, in 1911, but she committed suicide a year later.
Johnson, an avid auto and racing fan, died in an automobile accident in 1946.
Trump was joined by boxer Lennox Lewis and actor Sylvester Stallone as he announced the decision.
Open air Heavyweight World Championship fight between the reigning world champion Tommy Burns of Canada, left, and challenger Jack Johnson in front of 20,000 spectators at Rushcutters Bay near Sydney in 1908. The act banned the transportation of women in interstate or foreign commerce "for the objective of prostitution, debauchery or for any other immoral goal".
Iran presses European Union on measures to salvage nuclear deal
But he says it is up to the companies to decide: "We're not going to impose on French businesses to stay in Iran". They have said that as long as Tehran meets its commitments, they would remain in the deal.
During Johnson's heyday as a boxer, most of America's cities harbored brothels in so-called red light districts.
Seven decades later, Jack Johnson remains a towering figure in both sports and civil rights, an icon who turns up in rap songs, comic books and a gag line from Ron Burgundy in "Anchorman".
Linda E. Haywood, the great-great niece, wanted Barack Obama, the nation's first black president, to pardon Johnson, but Justice Department policy says "processing posthumous pardon petitions is grounded in the belief that the time of the officials involved in the clemency process is better spent on the pardon and commutation requests of living persons".
In a White House statement issued after the president signed Johnson's pardon, press secretary Sarah Huckabee Sanders reflected on the boxer's life and achievements, calling his conviction an "injustice".
He held on to that title until 1915 when Jess Willard, a white cowboy from Kansas, took the title with a knockout in the 26th round in Havana, Cuba.
Trump noted that a pardon for Johnson, whom he called "one of the greatest that ever lived", had considerable support in Congress, including within the Congressional Black Caucus. Others have taken up the cause célèbre as well including Senators John McCain, R-Arizona, Harry Reid, R-Nevada, and Orrin Hatch, R-Utah.
Out on bail pending appeal of the conviction, Johnson fled the country with Cameron and continued to fight overseas, including two defenses of the world title in Paris.