Orient's home game against Colchester United last weekend was suspended five minutes from time after fans invaded the pitch and staged a sit-down protest against owner Francesco Becchetti which lasted for more than an hour.
The fans were eventually sent home after being told that the game had been abandoned, only for the two teams to return to the field almost two hours after the stoppage to complete the match in front of empty stands.
Blackpool had been concerned that a similar incident could happen on Saturday, but the already-relegated O's will be allowed to bring 1,000 fans to the game - down 700 from the initial allocation.
"Following extensive discussions and representations made by relevant parties throughout the course of today, an agreement has been reached that delivers on the EFL's objective to ensure both sets of spectators can attend the match live," read a statement from the Leyton Orient Fans Trust.
"All remaining tickets sold to Leyton Orient supporters between now and Saturday's kick-off will be done so only on the basis that the purchaser is a current 2016-17 season ticket holder or a member of the Leyton Orient Fans Trust (LOFT). All tickets sold prior to Monday's suspension of sale remain valid."
An EFL spokesman added: "We are delighted we have been able to find an amicable solution to this particular issue and would like to place on record our thanks to all those parties who have assisted the EFL in achieving the outcome."
Leyton Orient's relegation from League Two this season ends a 112-year stay in the Football League.