The parents were arrested in December after being accused of hitting their children for not performing their prayers. They have been since been held on remand while their four children were taken by social services.
On Monday, the prosecutor filed charges of gross violation of their children's integrity (grov fridskränkning) and for assault.
"In my judgement, the information provided by the children via remote video interrogation is trustworthy," prosecutor Anna Arnell said in a statement.
"Together with other accompanying proof, such as witnesses and items that have been seized from the home, there are good grounds for the indictment."
The news came as a welcome relief to the mother of the children, who has struggled with life in a remand centre as the investigation proceeded.
"My client is relieved that the prosecutor has finally brought charges, as she will now be able to prove her innocence," Kristofer Stahre, the mother's defence lawyer, told The Local.
"She has been waiting a long time for this, it's been a tough time for her in jail, but now she is seeing the light at the end of the tunnel."
The trial is set to begin on February 18th and is expected to last ten days.
"It's difficult to speculate what will happen, but of course I hope my client will be freed. She hasn't done any of the things of which she's been accused," Stahre added.
The couple has lived in Sweden for three years. The father, Azizul Raheem Awalludin, works for Tourism Malaysia in Stockholm and has worked for his country's tourism ministry since 2000. His wife, Shalwati Nurshal, is a secondary school teacher on unpaid leave. The Swedish foreign ministry said neither Awalludin nor Nurshal are registered as diplomats, leading prosecutors to conclude that diplomatic immunity does not apply in the case.
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The case has stirred a heated reaction in Malaysia, where the four children were returned in early February. A Facebook group lobbying for the parents' return to Malaysia has almost 20,000 followers, and many took to Twitter to share their outrage alongside the hashtag #SwedenLetThemGo.
Kristofer Stahre has said the situation was the result of a "clash of cultures". Sweden was the first country in the world to outlaw corporal punishment back in 1979. In Muslim-majority Malaysia, corporal punishment is allowed in schools.
The case is not the first time a diplomat from abroad has got caught on the wrong side of the saw. In 2011, an Italian politician was convicted for assaulting his son during a Stockholm holiday, in a case that stirred heated debate in Sweden and Italy.