Timothy Storey, 35, formerly of Peckham, south London, groomed the girls at a religious summer camp where he was working, jurors were told.
He was found guilty of three counts of rape and one count of assault by penetration, following a trial at Woolwich Crown Court.
The former trainee vicar was remanded in custody to be sentenced at the same court on 15 April.
He was previously convicted in 2014 of grooming girls aged 10-16, but the offences for which he was most recently tried were committed in 2008 and 2009 and relate two women who are now in their 20s.
Storey befriended the girls "from an early age", the court heard, and sent them sexual texts and messages on social media. He sexually assaulted one girl on two separate occasions in 2008 and 2009 and assaulted the other girl at his home after taking her to a concert.
The victims contacted police about their ordeal following Storey's conviction in May 2014, for which he was ordered to serve three years in prison.
A spokeswoman for the Diocese of London said: "Timothy Storey has today been convicted of a series of appalling crimes and we are profoundly sorry for what his victims endured."
She said the diocese first received complaints about Storey in early 2009 and spoke to police before withdrawing him from ordination training.
Det Con Paul Hill, speaking after the conclusion of the trial on Thursday, said: "In his position as a youth leader he manipulated the victims and forced them to engage in sexual acts that they did not want to do.
"Storey thought he had got away with it, but the victims in this case were determined to see him brought to justice."
Police have urged any other victims of Storey to contact them with information.
A former church youth leader has been convicted of raping two teenagers.