Qatar Ports Management Company said direct services to Sohar and Salalah would operate three times a week.
Cargo for Qatar is usually shipped to ports in the United Arab Emirates and then loaded onto smaller vessels.
But last week the UAE, Saudi Arabia, Bahrain and Egypt severed economic and diplomatic ties with Qatar, alleging it supported terrorist groups and Iran.
Qatar has denied the charges and said the restrictions violate international law.
The tiny, oil- and gas-rich Gulf emirate is dependent on imports by land and sea for the basic needs of its population of 2.7 million.
On 5 June, the maritime authorities in Saudi Arabia, the UAE and Bahrain said they had closed their ports to Qatari-flagged vessels.
Dubai's massive Jebel Ali Port and Abu Dhabi Terminals also said they would not grant access to other vessels travelling to and from Qatar.
The world's largest container shipping line, Maersk Line, subsequently said it could not supply Qatar because the so-called "feeder" vessels it uses would no longer be able to transport cargo between the UAE and Doha.
On Sunday evening, the Qatar Ports Management Company (Mwani) announced that shipments would now be able to go through Oman, bypassing the UAE.
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"In light of the recent developments in the region, Mwani Qatar and its partners have ensured the business continuity of its ports and shipping operations in and out of Qatar to mitigate the impact of any action that would affect the imports and exports to and from the country," Al Jazeera quoted it as saying.
Oman is not among the Arab states that cut ties to Qatar, and has brokered secret negotiations between Western governments and Iran in the past.
Maersk Line immediately said it would accept new bookings for feeder shipments from Oman, with the first vessel scheduled to depart Salalah on 19 June and arrive in Doha on 25 June.
Despite the creation of the route, China's COSCO - the world's fourth-largest shipping line - announced it was suspending services to Qatar on Monday.
COSCO said it was acting "in view of the uncertainties as the situation develops" and "in order to protect the interests of customers", Reuters news agency reported.
When Qatar's isolation began last week there were reports of panic-buying in supermarkets amid fears of severe shortages.
But over the weekend, dairy products shipped by Turkish producers began arriving on shelves and five planeloads of fresh fruit and vegetables were despatched by Iran. Three ships carrying 350 tonnes (385 tons) of food are also set to leave Iran.
Qatar's foreign minister says 16% of Qatar's food supplies were transported across its land border with Saudi Arabia, which was closed last week. The crossing was also used for imports of building supplies and electronic equipment.
In a separate development on Monday, Abu Dhabi-based newspaper The National reported that the UAE would not deport Qataris married to Emirati nationals.
It came a day after the authorities in the UAE, Saudi Arabia and Bahrain said they were setting up hotlines to help families with Qatari members.