Rooney was fined by the club after being found guilty of drink-driving, and the two weeks' wages, reportedly around £300,000 will be donated to charity to benefit the local community.
The former England striker was also banned from driving for two years and ordered to do 100 hours of unpaid community work after appearing at Stockport Magistrates' Court on Monday.
The 31-year-old then faced a formal disciplinary at the club he re-joined in the summer and it is understood the striker was apologetic and totally accepted the consequences of his actions.
The club and player agreed that the financial penalty would be channeled into a range of programmes which are provided by Everton in the Community (EITC). This includes areas of health and well-being, mental health, youth engagement and employment and education.