It follows investigations into the deaths of Joy Robson at the Snowman Rally in Inverness in February 2013 and of John Leonard Stern, Elizabeth Allan and Iain John Provan at the Jim Clark Rally in the Borders in May 2014.
The FAI will go ahead under new legislation and is aimed at helping to avoid a repeat of such incidents.
The decision follows a change in the law which came into effect today which allows a single FAI to be held into deaths in different parts of Scotland.
A Crown Office spokeswoman said: "The two events hold similar questions in relation to spectator safety at rallies.
"The Lord Advocate considers it is in the public interest that these issues be explored together."
The date and location of the FAI are still being arranged.
The Crown Office said there will be no criminal proceedings in relation to either event, although that may be reconsidered "should additional evidence come to light".
It said FAIs were held into cases "where a death or deaths were sudden, suspicious, or unexplained or occurred in circumstances such as to give rise to serious public concern and where it appears to the Lord Advocate to be appropriate that an inquiry should be held into the circumstances".