Wodjan Ali Seraj Abdulrahim Shahrkhani, who will compete in the 78-kg category in judo, and teenager Sarah Attar will be the first Saudi women ever to take part after talks between the IOC and the country.
"This is very positive news and we will be delighted to welcome these two athletes in London in a few weeks time," said IOC President Jacques Rogge in a statement.
"The IOC has been striving to ensure a greater gender balance at the Olympic Games, and today's news can be seen as an encouraging evolution."
Thursday's decision means that every country competing in the July 27-August 12 Olympics will be represented by both male and female athletes.
At the Atlanta Games in 1996, 26 nations sent no female athletes, the figure falling to just three in Beijing in 2008.
In recent months human rights groups urged the IOC to ban Saudi Arabia from the Games unless it agreed to send women.
Powerful Saudi clerics denounce women for taking part in sport, saying it goes against their nature.
Women in Saudi Arabia are regarded as minors and require the permission of their guardian - father, brother, or husband - to leave the country and in some cases even to work. They are not allowed to drive.
Attar, 17, said she was honoured by the prospect of competing for her country at London 2012.
"A big inspiration for participating in the Olympic Games is being one of the first women for Saudi Arabia to be going," she told the Olympic Games website at her training base in San Diego, California.
"It's such a huge honour and I hope that it can really make some big strides for women over there to get more involved in sport."
In the Saudi city of Jeddah, Mariam Alawi, a housewife in her 20s, said: "This is fantastic news and it's about time. Maybe now people in Saudi can see that females are capable of taking the reins. The world already knows that women can do great things - maybe now Saudi can know that too."
Hashim Adnan, a 28-year-old Saudi man who works at an investment firm in Jeddah, said the athletes were likely to face "heavy criticism" in the country, but that the government should support them.
Saudi King Abdullah has a reputation as a cautious reformer and supporter of women's rights. Last year he announced plans to allow women to vote in municipal council elections and join the consultative Shoura council.
The country's official sports body, the General Presidency of Youth Welfare, only caters to male athletes and women do not take part in sports at state schools. So women athletes have to fund themselves and arrange their own training, mostly abroad.
A Saudi official told Reuters earlier this week Saudi women participating in the Olympics would have to obey the dress code of Islamic law. He did not elaborate, but other conservative Muslim countries have interpreted this to mean a headscarf, long sleeves and long pants.
Saudi Arabia is one of three countries, alongside Brunei and Qatar, never to have sent female athletes to the Olympics but the latter two confirmed earlier this year that their delegations would include women.
Brunei has entered Maziah Mahusin (athletics), while Qatar has entered Nada Arkaji (swimming), Noor Al-Malki (athletics), Aya Magdy (table tennis) and Bahiya Al-Hamad (shooting), who will also be her country's flag-bearer at the opening ceremony.
The IOC said the two Saudi athletes were entered by the Saudi Arabian Olympic Committee by the official deadline of July 9.