Gillespie was rushed in to bolster an attack already weakened by the absence of Michael Mason and including several other players with fitness concerns.
Daniel Vettori, Shane Bond and Jacob Oram have all just recovered from injuries while all-rounder Scott Styris is still on the sick list after injuring his back playing for Middlesex.
''This is the strongest squad we can out together for what is a major tournament at the start of an intensive One-day series,'' New Zealand coach John Bracewell said in a statement.
The selection of Gillespie was the only real surprise in the 14-man squad but Bracewell said he was confident the 26-year-old would handle the step up to international cricket.
Gillespie has been a solid performer for Wellington in the domestic first-class competition and impressed the national selectors with his strong displays for New Zealand A earlier this year.
''He thoroughly deserves his place in the squad and his skills as a specialist death bowler will extend our depth in this area,'' Bracewell told New Zealand Press Association.
''He's a new-ball bowler who ends up bowling three or four at the end.'' Vettori, Bond and Oram were all cleared to play but Styris remains a concern after missing his last county match in England.
Bracewell said he was hopeful Styris would play but he was not certain.
''We will take a wait-and-see approach before considering whether he can tour and have no need to consider a replacement at this stage,'' Bracewell said.
The preliminary phase of the Champions Trophy begins on October 7 with the group stage starting on October 15.
New Zealand, who won the tournament in 2000 when it was known as the ICC Knock Out, are in Group B with South Africa, Pakistan and a qualifier yet to be decided.
New Zealand squad: Stephen Fleming (captain), Nathan Astle, Shane Bond, James Franklin, Peter Fulton, Mark Gillespie, Brendon McCullum, Hamish Marshall, Kyle Mills, Jacob Oram, Jeetan Patel, Scott Styris, Daniel Vettori, Lou Vincent.