The game still enters the record books as the toss took place before it rained, the International Cricket Council (ICC) said in a news release.
That means the 43-year-old Bowden, with the famous crooked-finger send-off for batsmen, becomes only the second New Zealander after Steve Dunne to stand in a century of one-day internationals.
"All I ever want is to ensure I do my best, it is not about records," said Bowden. "Having said that, it is a special day and it is great to be a member of the 100-club."
He is the youngest umpire to join the club but it is a record he is likely to hold for only a few days.
Simon Taufel, 35, is one short of his century and should reach the milestone in his native Australia during this month's tri-series
"Shortly after I stopped playing in 1986 due to arthritis, I realised I wanted to give something back to the game and the way I chose to do that was to umpire," said Bowden.
Most one-day international appearances by umpires:
David Shepherd (England) 172
Rudi Koertzen (South Africa) 158
Steve Bucknor (West Indies) 151
Daryl Harper (Australia) 127
Darrell Hair (Australia) 124
David Orchard (Australia) 107
Steve Dunne (New Zealand) 100
Billy Bowden (New Zealand) 100