EFL chairman Rick Parry says the decision is a “lifeline” for lower-league clubs.
Rooney was visited by a friend who had been instructed to be tested for Covid-19 and was later found to have the disease.
The Lincolnshire club has players and staff still self-isolating.
The five-substitute proposal was first put forward by FIFA earlier this year.
Boro boss Neil Warnock tested positive on Thursday.
The midfielder is battling a back injury and will not be available for the Canaries.
The first matches take place this weekend at clubs including Middlesbrough and Blackpool. March this weekend as the EFL carries out seven pilot events.
The 71-year-old Warnock did not take charge of Boro’s 2-0 Carabao Cup second-round defeat at home to Barnsley on Wednesday after feeling unwell upon arriving.
The clubs held fresh discussions with the EFL on Wednesday and it was decided to look again at scheduling options at the end of the year, with a view to playing the match in 2021 in front of as many supporters as is safely possible.
The government is reviewing a plan to allow a limited number of spectators back into sports venues from October 1.EFL chairman Rick Parry,head of policy John Nagle