The fire, which started a few hours after Gareth Southgate's squad had been training at the 3300-capacity stadium, caused thick black smoke and was dealt with by fire crews.
A television gantry went up in flames while a video assistant referee (VAR) monitor and a dugout appeared to be damaged. Some of the playing surface towards the touchline was also burned.
However, FAF has moved to allay fears that the fixture is at risk of being postponed or moved to a new venue.
"No personal harm has been reported, only material damage. The schedule will continue as planned and the match will go ahead," a statement read on Saturday (AEDT).
UEFA is expected to have the final say on whether the game will take place at Estadi Nacional.
England leads the way at the top of Group I ahead of this weekend's contest, sitting four points clear of second-place Albania and a further point in front of Poland.