Saudi Arabia is Japan's biggest oil supplier and Japanese refineries and other oil importers bought about $2.2 billion worth of Saudi oil in January.
It identified nine main areas of cooperation, including competitive industry, energy, health care and medicine, high-quality social infrastructure and investment and finance.
In the joint statement, the two countries also pledged to pursue synergy effects of Saudi Vision 2030 and Abe's growth strategies for Japan.
Approximately 10 aircraft were used to transport the huge delegation to Japan, a local government official said, while over 1,000 rooms at high-end hotels in Tokyo have been reserved and some 500 limousines mobilised for the delegation, a Saudi government source said.
A document for cooperation signed by Japan and Saudi Arabia on Monday indicated that the two countries will move to strengthen economic ties.
When Prince Mohammed visited Tokyo last September, Abe assured him that Japan was keen to participate.
"Direct and secondary economic effects are expected", Sakakibara Sadayuki, chairman of the Japan Business Federation, or Keidanren, told reporters on Monday.
Last month, the Saudi monarch went to Indonesia on his first trip outside the Middle East and North Africa since he visited the U.S. in 2015.
A follow-up ministerial meeting is set for Tuesday, to lay out the details of the collaboration.
The trip to Japan by the 81-year-old is the first visit by a Saudi king in 46 years.
India and Saudi Arabia are considering possibilities of joint production in defence industry.
"We are looking forward to the visit of the King of Saudi Arabia later this year", External Affairs Secretary (Economic Relations) Amar Sinha, said at an event organised by the Saudi petrochemicals giant SABIC.
The Saudi monarch arrived in Japan on Sunday after a visit to Malaysia and Indonesia that included a holiday stay in Bali.
They include more than 1,000 Cabinet ministers, corporate executives and royal family members.