Bonifay's father was a minor league general manager for several teams in the farm systems of the Detroit Tigers and Cincinnati Reds. His own career in sports began as a football placekicker and third baseman at Georgia Tech in the early 1970s. While at Georgia Tech, Bonifay set and tied many records in football as well as baseball as well as being named an All-American Honorable Mention in baseball. Bonifay was not drafted but signed on as an undrafted free agent with the St. Louis Cardinals and played two years of Minor League Baseball. Bonifay stopped playing after he was plagued with knee problems.
Bonifay went back to Georgia Tech and became an Assistant Coach under Jim Morris beginning in 1985. In 1989, Bonifay was inducted into the Georgia Tech Sports Hall of Fame for his achievements in baseball. Bonifay is still the youngest person ever inducted into the Georgia Tech Sports Hall of Fame. In late 1987, Bonifay became a scout with the Cincinnati Reds starting his stint working in several major league baseball front offices.
In 1993, he became General Manager of the Pittsburgh Pirates and in 1997, he was named General Manager of the year. Bonifay is most remembered by Pirates fans for giving out large contracts to washed up players. Perhaps his most infamous moment came in 2000, when he signed catcher Jason Kendall to a 6-year $60 million contract, a move that would have severe financial ramifications on the Pirates in later years.  Bonifay was also heavily criticized for the two-year, $10-million contract given to Derek "Operation Shutdown" Bell in 2001.
Bonifay was responsible for a few good trades such as trading Ricardo Rincon for Brian Giles before the 1999 season. During his tenure as GM with the Pirates, Bonifay never compiled a winning season, however in 1997 the team remained competitive until the final week of the season and finished in 2nd place with a 79-83 record on just a $9 million payroll. At the beginning of the 1997 season, most analysts picked the Pirates to finish last with over 100 losses.
After he was fired in 2001 by Pirates owner Kevin McClatchy, Bonifay signed with the Tampa Bay Devil Rays as their director of player development and scouting. He was released from that position in the offseason of 2005 when the Rays were sold into new ownership. Bonifay signed on with the St. Louis Cardinals as a pro scout for two years starting in the 2007 season. Now, Bonifay works for the Cincinnati Reds as a Special Assistant to the General Manager.
His sons Johnathan and Josh both played baseball in college. Johnathan played for Wake Forest and Josh played for UNC Wilmington. Josh played seven years in Minor League Baseball for the Pittsburgh Pirates and the Houston Astros. Josh is now a hitting coach for the Pittsburgh Pirates minor league system.
- Barzilla, Scott (2004). The State of Baseball Management: Decision-Making in the Best and Worst Teams, 1993-2003. McFarland & Company. pp. 185–186.<templatestyles src="Module:Citation/CS1/styles.css"></templatestyles>
- Baseball America -- baseball executive database listing
- Georgia Tech alumni profile (1999)
- Pittsburgh Post-Gazette interview with Bonifay, June 2005
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