In a written veto issued Wednesday, Nixon said the lack of an exemption for rape and incest victims forced him to quash the bill, which cleared the legislature in May.
"This glaring omission is wholly insensitive to women who find themselves in horrific circumstances, and demonstrates a callous disregard for their well-being," Nixon wrote.
Missouri law currently requires a 24-hour waiting period before an abortion can be performed. If the bill had become law, it would have made Missouri home to some of the nation's strictest abortion legislation.
Only Utah and South Dakota require citizens to wait 72 hours to receive an abortion, and only in South Dakota are victims of rape and incest not given an exemption from the law, Nixon said.
Even if the bill had included exemptions for rape and incest victims, Nixon said he still would have vetoed the legislation.
"Lengthening the mandate to 'at least' 72 hours serves no demonstrable purpose," Nixon wrote.
Republican state Sen. David Sater, a sponsor of the Senate bill, said he was extremely disappointed in Nixon's decision and accused the governor of playing politics with a life-and-death matter.
"This is an irreversible and permanent decision, and taking the time to think about the consequences is not unreasonable or a burden. Gov. Nixon decides to be pro-life or pro-choice depending on the next election," Sater said in a statement. "Serious elected officials remember that unborn children are not abstractions to play politics with."