U.S. District Judge Richard Casey granted a request by the National Abortion Federation and seven doctors to block enforcement of the ban.
The ruling applies only to the plaintiffs, but it could have broad application. The federation says that its members perform half of the abortions done nationwide.
The decision follows a separate ruling by a federal judge in Nebraska who also blocked the law Wednesday — less than an hour after Mr. Bush enacted the law. That ruling covers four doctors, who together are licensed in 13 states across the Midwest and East, and their staffs.
Casey noted in a three-page order that the plaintiffs would suffer irreparable harm without a court injunction.
He said the government made clear at a hearing Wednesday that the medical community is conflicted as to whether the procedures covered by the law are necessary to protect a woman's health and that Congress did not find a consensus.
"Given the (government's) position, the court is constrained, at this time, to conclude that it is substantially likely that plaintiffs will succeed on the merits," Casey wrote.
Vicki Saporta, president and chief executive officer of the National Abortion Federation, which is represented by the American Civil Liberties Union in its challenge, said she was pleased "that the court acted quickly to protect women and their doctors."
"Allowing Congress to practice medicine without a license endangers the lives and health of women," Saporta said. "Thankfully, the court understood the gravity of the situation and stopped this law from taking effect."
"It's not unusual for a law like this to be challenged," says CBSNews.com Legal Analyst Andrew Cohen, "and certainly the lawmakers who drafted it should have known that some judges would find it unconstitutional."
Cohen adds: "The question is whether federal appeals court judges are going to do the same and whether the U.S. Supreme Court ultimately decides to get involved."
The law that Mr. Bush signed, similar to ones former President Clinton twice vetoed, bans certain procedures on fetuses that are partially delivered, and then killed. The technique is used during the second and, occasionally, third trimester of pregnancy.
Recent polls show that as many as seven out of 10 Americans think such practices should be illegal. Final passage in the Senate last month was by a lopsided 64-34 vote, with 17 Democrats, including Minority Leader Tom Daschle of South Dakota, supporting the ban.
Mr. Bush called the procedure Wednesday "a terrible form of violence…directed against children who are inches from birth."
Still, the nation remains much more evenly divided on the broader issue of whether the Roe v. Wade decision should remain in force. Mr. Bush acknowledged as much last week when he told reporters: "I don't think the culture has changed to the extent that the American people or the Congress would totally ban abortions."
Abortion-rights advocates used Wednesday's bill-signing to mount a broader campaign.
"What this is about is a direct stab at Roe v. Wade. It's a direct stab to roll back or whittle away at a woman's right to choose," said Rep. Carolyn Maloney, D-N.Y.