The ruling by Polk County Judge Jeffrey Farrell was prompted by Gov. Terry Branstad's announcement that he will sign a bill into law Friday that includes the waiting period.
After a lower court denied its request for an injunction on Thursday afternoon, Planned Parenthood of the Heartland successfully appealed to the Iowa Supreme Court.
Attorneys for Planned Parenthood and the ACLU argued the stay was needed because women who had existing appointments to obtain abortions were immediately restrained from getting them according to their scheduled appointments.
Beside the waiting period, it would outlaw most abortions after 20 weeks of pregnancy and wouldn't allow exceptions for rape, incest or fatal fetal anomalies.
Alice Clapman, a lawyer for the Planned Parenthood Federation of America, says 44 scheduled procedures will be made illegal if Branstad signs the bill as planned.
Planned Parenthood clinics also had 11 medication abortion patients scheduled for Tuesday and 28 for Wednesday, including 19 medication abortion patients.
Branstad told reporters he was encouraged by the district judge's swift decision the day before, saying "it's pretty unusual that someone would bring a legal challenge before a bill is even signed, but I think the district judge did the right thing".
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Iowa becomes one of three states with a 72-hour waiting period and two-trip requirement for abortions - joining Missouri and South Dakota. A signing ceremony is slated for 8:30 a.m., at the state Capitol building.
When asked earlier about efforts to block to law, Branstad noted that similar abortion restrictions have been upheld in other states.
On Thursday, Gov. Branstad praised state lawmakers for passing the law.
Iowa Secretary of State Paul Pate assures Iowans that voting participation will maintain its high standard nationally, and maybe build upon it under this new law.
Women in the United States have the right under the Constitution to end a pregnancy, but abortion opponents have pushed for tougher regulations, particularly in conservative states.
The new Iowa law helps to ensure that women receive information about the abortion and their unborn baby, as well as time to consider that information before making an irreversible decision about their baby's life.