Everton fans invade the pitch
Concerns were raised about safety at grounds after a number of pitch invasions at the end of last season.
Individuals who carry or use pyrotechnics or smoke bombs will also be banned and identified offenders will be reported to the police.
The Football Association will also implement tougher sanctions for clubs.
It is an offence for fans to enter the pitch "without lawful authority or lawful excuse" under the Football Offences Act 1991 - but offenders have not always been prosecuted.
However, prosecuting offenders will now be the "default response" under the new measures.
The leagues and the FA will:
The Premier League, EFL and FA will also work with police forces to "establish a new principle for cases relating to pyrotechnics and smoke bombs".
Premier League clubs agreed new measures to deal with pitch invasions last month following a series of incidents.
Aston Villa keeper Robin Olsen was assaulted at Manchester City on the final day of the season, while a Nottingham Forest fan was jailed for headbutting Sheffield United captain Billy Sharp at the end of their play-off match.
"The rise in anti-social behaviour that we saw in stadiums at the end of last season was entirely unacceptable and put people's safety at risk," FA chief executive Mark Bullingham said.
"Together, English football has introduced new measures and stronger sanctions, for the start of the coming season, to send out a clear message that we will not tolerate this type of illegal and dangerous behaviour.
"It is the responsibility of everyone in the game, including governing bodies, clubs, players, coaches, and fans, to ensure that we all play our part in protecting our game and each other."
Kevin Miles, chief executive of the Football Supporters' Association, added: "We are contacted by supporters on a fairly regular basis who have been caught jumping on the pitch, or with pyro in the stands, and without exception they regret doing it.
"Whether they had positive intentions or not is irrelevant in the eyes of the law - pyro and pitch incursions are illegal, you will be prosecuted and you will be banned by your club."
-- Courtesy of BBC Sport