CVS — America's biggest pharmacy chain — said it still had enough of the pills that can prevent pregnancy in stock but wanted to ensure "equitable access."
The new guidelines affect Plan B pills, sold for $49.99 each, and the Aftera brand retailed at $39.99.
Rite Aid — more than 2,500 pharmacies across northern states — said "increased demand" forced it to limit the sales of Plan B and Option 2, sold at $32.99.
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The Supreme Court's ruling to overturn Roe v Wade — which supported abortion in the constitution — has caused nationwide stress, with many women running to stock up on pills.
A justice has suggested they could also re-examine rulings on contraception, although at present there is no suggestion that any state will block the sale of "morning after" pills.
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Morning after pills are emergency contraception reserved for after unprotected sex or as a last resort when other devices — like condoms — have failed.
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They are available over the counter, with one pill that ought to be taken within 72 hours of intercourse in order to stop a pregnancy.
It works by preventing ovulation or altering the lining of the womb to stop an egg from becoming implanted.
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The pills are about 87 percent effective, manufacturer data shows.
They differ from abortion pills — such as Mifeprex — which require a prescription and involve taking two different pills ten weeks apart.
Many women may only buy one packet of "morning after" pills at a time, with those who purchase more looking to stock up.
CVS put the limit in place on Saturday, and Rite Aid followed suit on Monday.
A spokeswoman for CVS said they saw a "sharp increase" in sales immediately after the ruling, triggering the limit.
However, as sales have "returned to normal," they are in the process of removing the restriction.
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They added: "We continue to have ample supply of emergency contraceptives to meet customer needs."
Rite Aid also has Plan B pills for $47.49 each and Option 2 pills for $32.99 for one.
Walgreens said it could still meet "in store demand" and was "working" to re-stock its online inventory. The pharmacy did not say when it sold out of home-delivery pills.
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Other pharmacies — including Walmart — are yet to put restrictions on the sale of "morning after" pills in place.
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It comes as women hurriedly stockpile abortion pills and contraception over fears that access could be banned.
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Last week the court's longest-serving justice Clarence Thomas warned that they could "reconsider" rulings on access to contraception suggesting the right to the 'morning after' pill could also be at risk.
This has sparked panic in many circles, with women now hurrying to restock.
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In the days since Roe v Wade was overturned some clinics say their appointments have spiked four-fold since the Roe v Wade ruling.
Abortion organization Planned Parenthood Southeast, in Atlanta, Georgia, also says they have faced a wave of women wishing to know how many pills are available.
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Still, amid the rush many are being advised not to completely "clear the shelves" of abortion pills to ensure they remain available for women who need them right now.
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It is expected that abortion pills will become the direction of many legal battles in the states to outlaw abortion.
In total, 13 states have already imposed new laws, with Alabama, Arkansas, Kentucky, Louisiana, and Missouri altogether banning them with no exceptions for rape or incest.
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