Coonelly, 47, takes over for Kevin McClatchy, who had been the Pirates' primary owner and president since 1996. McClatchy announced two months ago that he was stepping down at the end of the season.
"Frank brings a tremendous amount of baseball experience to this role. This experience will be a critical asset for us moving forward, including in the short term in the selecting of our new general manager and assembling our baseball operations team," said Pirates Chairman of the Board Bob Nutting.
One of Coonelly first duties will be to find a replacement for General Manager Dave Littlefield, who was recently fired as Pittsburgh was headed for its 15th consecutive sub-.500 season.
Coonelly gained a reputation as a tough negotiator while in the commissioner’s office where he was involved in labor negotiations with players and umpires and salary arbitration.