Taylor, 32, registered his 17th ODI century with an unbeaten 102 as New Zealand posted 289-4.
It took him past all-rounder Nathan Astle, who made 16 one-day centuries from 1995-2007.
Seamers Trent Boult and Tim Southee then restricted South Africa to 283-9 to level the five-match series at 1-1.
Former Test captain Taylor also became the country's quickest batsman to 6,000 runs in the 50-over format as he struck eight boundaries in his 110-ball innings.
"Nath was one of my idols growing up so I was fortunate towards the end of his career and start of mine to play with him," Taylor said.
"It's a little bit embarrassing from that point of view but records are there to be broken and hopefully someone will beat mine."
Ross Taylor became New Zealand's leading one-day international centurion as the Black Caps beat South Africa by six runs in Christchurch.