The decree was due to expire on Wednesday.
Since April 19, the borders have been closed except for essential travel.
These include, but are not limited to, travel for work or to obtain medical care, returning home to Ontario or even a trip to care for a sick person.
People arriving from Quebec or Manitoba must stop and present identity papers when requested by an officer.
The latter can order them to return to their province, if he judges that they have no valid reason to come to Ontario.
Eight other provincial decrees are also extended until June 16. These include the transfer of patients, the reassignment of health service personnel and the ban on recreational camping on public lands.
The Ontario government unveiled its three-step deconfinement plan.
However, it did not specify when the interprovincial borders would reopen.
It also did not contain any provisions on schools. One month away from the end of classes, the province has still not announced if in-person teaching would resume.
Ontario counted on Saturday 1057 new cases of COVID-19. On Thursday, the chief medical officer of the province admitted that the situation was improving, but not enough, in his opinion, to anticipate deconfinement.
The province planned to take the first step in mid-June, if a number of conditions were met.