In the beginning of his sophomore year in 1966, Jackson replaced Rick Monday (the first player ever selected in the Major League Baseball draft and a future teammate with the A's) at center field. He broke the team record for most home runs in a single season, led the team in numerous other categories and was first team All-American. Many scouts were looking at him play, including Tom Greenwade of the New York Yankees (who discovered Mickey Mantle), and Danny Murtaugh of the Pittsburgh Pirates. In his final game at Arizona State, he showed his potential by being only a triple away from hitting for the cycle, making a sliding catch, and having an assist at home plate. Jackson was the first college player to hit a home run out of Phoenix Municipal Stadium.
In the 1966 Major League Baseball draft on June 7, Jackson was selected by the Kansas City Athletics. He was the second overall pick, behind 17-year-old catcher Steve Chilcott, who was taken by the New York Mets. According to Jackson, Winkles told him that the Mets did not select him because he had a white girlfriend. Winkles later denied the story, stating that he did not know the reason why Jackson was not drafted by the Mets. It was later confirmed by Joe McDonald that the Mets drafted Chilcott because of need, the person running the Mets at the time was George Weiss, so the true motive may never be known.
Jackson played for two Class A teams in 1966, with the Broncs for just 12 games, and then 56 games with Modesto in the California League, where he hit 21 homers. He began 1967 with the Birmingham A's in the Double-A Southern League in Birmingham, Alabama, where Jackson got his first taste of racism, being one of only a few blacks on the team. He credits the team's manager at the time, John McNamara, for helping him through that difficult season.