Lieutenants Maxine Stiles, Alexandra Olsson and Penny Thackray earned their "Dolphins" after months of training, including operations on HMS Vigilant.
Defence Secretary Philip Hammond hailed their "huge personal achievement" and said it was "an historic moment for the Royal Navy and our armed forces".
A ban on women submariners based on health fears was lifted in 2011.
A review of concerns that submarines' higher levels of carbon dioxide could carry risks to female health decided the fears were unfounded, the BBC reported.
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"I felt like a little sister to 165 brothers," she said.
"Of course it's been challenging, but women are absolutely capable of doing this job. I think that change can always be a bit of a shock, but I look forward to seeing more and more women getting on board," Olsson said.
Lt Stiles, 29, said: "As long as you can do your job and you're good at what you do, I don't think they [the crew] cared whether you were male or female."
"I just forgot the outside world - you get a whole new world," said the 39-year-old from West Yorkshire.
Stiles will continue as a logistics officer on board HMS Vigilant, while Olsson is undertaking deputy weapons engineering officer training. Thackray is due to become an education officer.
HMS Vigilant's commanding officer, Cdr Matt Dennis, said: "I was impressed with how seamlessly the three women integrated on board."
Second Sea Lord Vice Admiral David Steel said: "Women have been serving in ships at sea with the Royal Navy for more than 20 years and integrating them into the Submarine Service completes their inclusion into all seagoing branches."