Samuel Johnson, from Reydon, Suffolk, and Patrick Hart, from Brislington, Bristol, were charged with aggravated trespass and criminal damage.
Orange paint powder was scattered across the pitch midway through the first half of the match in south-west London between Saracens and Sale.
Stewards removed the pair from the pitch to a mix of boos and cheers from fans, and the game resumed.
It was the latest event to be affected by Just Stop Oil after a similar incident at the Chelsea flower show.
A statement from the group later confirmed the men involved in the protest were Dr Patrick Hart, 37-year-old GP, and Sam Johnson, 40, a construction worker.
The Metropolitan Police said: ‘The charges relate to an incident on Saturday, May 27 when orange powder was thrown on the pitch 24 minutes into the rugby game during live play briefly disrupting the competition for players and spectators.’
Both Johnson and Hart were remanded in custody and will appear at Wimbledon Magistrates’ Court on Monday.
Kyle Gordon of the Met, Gold Commander for events in London on the day, said: ‘To date we have seen 102 slow marches across London by Just Stop Oil that has caused serious disruption and frustration to those going about their business in the city leading to 51 arrests to date.
‘Similarly, yesterday’s incident at the rugby final will have caused frustration to both the players and spectators alike.
‘With many other events taking place, and visitors in our capital this weekend, we will continue to monitor and respond to such incidents quickly.
‘Where protest moves into criminality or serious disruption, we will take robust action to ensure Londoners and visitors alike can continue to enjoy their Bank Holiday weekend.’
Get in touch with our news team by emailing us at [email protected].
For more stories like this, check our news page.