Gaffney first tweeted about the decision over the weekend and the school confirmed it late Monday afternoon. Gaffney was drafted in the 24th round by the Pittsburgh Pirates in last month's MLB First-Year Player Draft.
"Every athlete dreams of the opportunities that I have been afforded, first at Stanford, and now with Pittsburgh," Gaffney said in a statement. "Every day of the last three years has prepared me for the chance to compete professionally, and I cannot thank enough the coaches and professors who have worked with me."
Gaffney started the 2011 season as the third back behind starter Stepfan Taylor and Anthony Wilkerson, but quickly gained more carries and eventually moved up as the No. 2 back. He also carved out a niche as Stanford's Wildcat back.
Last season he rushed for 449 yards and seven touchdowns. For his career, he ran for 815 yards on 156 attempts and 12 touchdowns.
In December, Gaffney said he would have to be a "top tier" draft pick in order for him to leave college early.
"It would take a good amount for me not to come back next year," he said. "... There are no more Bo Jacksons in the world. The two professional sports thing isn't really going to happen. In the next year or two I'm going to have to make a decision. Wherever my best opportunity is, that's what I'm going to chose."
This past season, he started 30 games in left field for Stanford and 16 in center, hitting .245 with two home runs, 17 RBI and 48 runs scored in 54 games.
Gaffney's departure is a sizeable dent to Stanford's running back depth, but it's also one of the Cardinal's strongest positions so they should be able to absorb the loss. Wilkerson has the opportunity to re-claim his spot behind Taylor, a back-to-back 1,000-yard rusher who carried 242 times last season for 1,322 yards and 10 touchdowns. Ricky Seale also emerged in the spring with a strong showing, Kelsey Young has looked impressive and touted-recruit Barry Sanders enters the program in the fall.
In the statement, Gaffney, who was recruited out of Cathedral Catholic High School in San Diego, noted his appreciation to Jim Harbaugh and Stanford baseball coach Mark Marquess for recruiting him. He also thanked current Stanford coach David Shaw for allowing him to continue to play both sports.
"I thank the Pittsburgh organization for providing me this opportunity and I am excited to begin my professional career," he said.
Gaffney will return to Stanford in the offseason to complete his degree in sociology.