The retailer has announced it will be removing the dolls from their shelves.
A mother from Florida launched an online petition for their sale to be stopped by the chain, as the dolls were a "dangerous deviation from their family friendly values".
In a statement Toys R Us said: "Let's just say, the action figures have taken an indefinite sabbatical."
The four collectible dolls, based on characters from the AMC drama, and carried accessories including a detachable bag of money and a bag of methamphetamines.
Toys R Us had said that the figures were sold in limited quantities in the adult-action-figure area of its shops and had already removed them from sale in their online store.
"While the show may be compelling viewing for adults, its violent content and celebration of the drug trade make this collection unsuitable to be sold alongside Barbie dolls and Disney characters," said campaigner Susan Schrivjer.
Her petition has now gathered more than 9,000 signatures.
Another campaign has been launched in response by Daniel Pickett, of Manhattan Beach, California, who wants Toys R Us to keep the dolls on sale. It has more than 3,000 signatures.
"I'm a parent of a school aged child myself, but I'm an informed, responsible parent and I closely monitor the toys, TV, music, movies and games that my daughter sees, he said.
"That's my job, and I take it seriously. But I also like toys/action figures and I want 3D representations of characters from my favourite properties and I love being able to walk into a store and find them."
Breaking Bad follows the story of Walter White, a high school chemistry teacher, played by Bryan Cranston, who becomes a crystal meth dealer.
Earlier this week Cranston tweeted in response to the petition.
"'Florida mom petitions against Toys 'R Us over Breaking Bad action figures.' I'm so mad, I'm burning my Florida Mom action figure in protest," he wrote.
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Breaking Bad fans will have to go somewhere other than Toys R Us to buy character action figures.