The English Football League (EFL) backed Blackpool's request to suspend ticket sales to allow "a full review" of safety and security arrangements.
O's fans have now been allocated 1,000 tickets, down from an original total of 1,700, for Sunday's match.
All travelling supporters must be a season-ticket holder or member of the Leyton Orient Fans' Trust (LOFT).
On Saturday, Orient fan protests against club president Francesco Becchetti, delayed their defeat by Colchester by two hours, while Blackpool's final game of the Championship season in May 2015 had to be abandoned after a pitch invasion.
Fans of Blackpool and Orient also joined together to march against their respective owners when the clubs met earlier in the season, after collaboration between LOFT and Blackpool Supporters Trust.
A LOFT statement said the Trust was pleased that common sense had now prevailed over the suspension of ticket sales, but continued: "It is unfortunate that this could not have been resolved between Blackpool FC and the EFL without causing O's fans 24 hours of worry and anger."
The statement continued: "We feel that no restrictions beyond those which would ordinarily be in place for such a fixture are necessary, nor should it be necessary to restrict the number of tickets available to O's supporters."
All tickets sold before Monday's suspension are still valid.
An EFL spokesperson said it was "delighted we have been able to find an amicable solution to this particular issue".
Leyton Orient fans have been given a reduced ticket allocation for their final game of the season at Blackpool.