The women's football season from tiers three to seven has also been brought to an end, with results declared null and void, while all grassroots leagues have also been ended prematurely due to the Covid-19 outbreak.
The FA said it was continuing to work with the National League to conclude their season, with the league's board meeting twice meeting via video link on Thursday, in a bid to reach an agreement on how to conclude the campaign, without declaring it void.
The FA said the WSL and Women's Championship will continue towards a conclusion "as quickly as possible".
The FA said the decision to end steps 3 and below of the English non-league pyramid had been made "in the best interests of the game and in consultation across key stakeholders" but it is likely to leave some clubs furious and raises the possibility of legal challenges from clubs who were already technically promoted or some way clear at the table.
The governing body added that it was committed to completing its competitions, including the FA Cup, "whenever it is safe and appropriate to do so" and said it was continuing to plan for next season's cup competitions.
In a statement, the FA said: "These are challenging circumstances for English football and all decisions taken are in the best interests of the game," said a Football Association statement.
"Our primary concern will always be for the safety and welfare of clubs, players, staff, officials, volunteers and supporters during this unprecedented time.
"Today's steps take into account the financial impact during this uncertain period, whilst considering the fairest method on how the sporting outcomes for the season will be decided, with the integrity of the leagues in mind.
"With the 2019-20 Emirates FA Cup, Women’s FA Cup, Buildbase FA Trophy and Buildbase FA Vase all at advanced stages, we are reviewing all options as we seek to complete these competitions whenever it is safe and appropriate to do so. Clubs involved are close to reaching a major final and for those clubs and supporters we will do all we can to keep the Wembley dream alive.
"In respect of The FA Youth Cup, The FA County Youth Cup, The FA Sunday Cup and The FA Inter-League Cup, we are also seeking to complete these competitions if it is feasible to do so."