The deal, which was first reported by Baseball America, will allow Alford to continue playing football at Southern Mississippi University, but he will join one of Toronto's Minor League affiliates this summer.
Alford, who was considered a difficult sign because of his commitment to Southern Mississippi, will fly to Florida on Saturday to meet with the Blue Jays.
"I will play football and I will play baseball," said Alford in a phone interview.
Alford wouldn't reveal the details of the contract but expects to sign by Monday. He will likely be paid over the recommended slot of $424,400 for the No. 112 overall pick.
Alford reportedly told teams prior to the Draft to not select him because of his desire to continue playing football, which is the only reason he dropped to the third round. The center fielder was considered a first-round talent and was ranked by MLB.com as the No. 56 prospect entering the Draft.
Larry Watkins, Alford's high school coach, told MLB.com earlier in the week that Toronto scouted him heavily all season.
Blue Jays amateur scouting director Andrew Tinnish raved about Alford in a conference call with reporters on Wednesday.
"Obviously he's a very good athlete and a very good kid, with a very short and quick compact swing," Tinnish said. "He's probably a seven runner on our two-to-eight scale. He's very explosive. He's a guy that we'd love to have as part of our organization."
The toolsy outfielder has already started taking classes at Southern Mississippi, where he is studying business.
Alford started all four years he played at Petal High School (Miss.), and helped the team win state championships in his sophomore and junior years.
Last season, in his senior year, Alford hit .483/.569/.793 with four home runs while stealing 14 bases in as many attempts.
Chris Toman is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.