Paul Hill, 49, died by lethal injection as dozens of his supporters gathered outside the prison and hailed him as a hero.
Seconds before the injection was given, Hill smiled and said: "May God help the unborn child." Six minutes later he was officially declared dead.
Hill was unrepentant till the very end and said on the eve of his execution that he had no regrets and expected to be rewarded by God for preventing an abortion doctor from killing any more unborn babies.
The former Christian pastor and a father of three, Hill had in 1994 shot dead a doctor John Britton and his bodyguard James Barrett outside an abortion clinic in Pensacola, Florida.
Shortly before being executed, Hill told journalists that in slaying Britton he prevented the doctor from killing more unborn babies.
"Instead of being shocked, more people should do what I did," Hill said.
"I expect a great reward in heaven," he added.
His execution came amid tight security arrangements around the prison as far-right anti-abortion groups staged a noisy demonstration outside.
Opponents of the death-penalty also lobbied against the execution, saying it would turn Hill into a martyr for those who considered slaying abortion providers as "justifiable homicide."
"Instead of being shocked, more people should do what I did"
The slain doctor's step-daughter, Catherine Fairbanks had also asked for a stay on the execution, saying Hill must be suffering from a personality disorder and should not be turned into a martyr.
Opposed to abortion, Florida Governor, Jeb Bush – brother of President George Bush - had made it clear he had not intention of granting a pardon.
"I believe in the protecting of innocent life. I also believe it is not inconsistent to suggest that when a person in a premeditated fashion … murders two people and he is convicted to death, that carrying out that sentence is appropriate," the governor said.
Far-right anti-abortion groups hailed Hill as a hero.
"What Paul did was the correct thing to do. He did what God called him to do," Don Spitz, a pastor who heads the pro-life Virginia Anti-Abortion group said.