Gibbons' decision to remain with the Royals was first reported by the Kansas City Star on Thursday afternoon.
"Who knows who will get that job [in Pittsburgh]?" Gibbons told the Star. "I just had a feeling that I might be better off staying in Kansas City."
Gibbons was one of seven candidates the Pirates have interviewed. Eric Wedge, their first interview, agreed to become the manager of the Seattle Mariners.
The Pirates also interviewed bench coach Jeff Banister, Ken Macha, Bo Porter, Dale Sveum and Carlos Tosca. Gibbons replaced Tosca in Toronto in 2004.
Gibbons, who met with the Pirates on Oct. 11, spent parts of five seasons managing the Blue Jays and led Toronto to a 305-305 record during that span. He has served as the Royals' bench coach since the start of the 2009 season.