Akinfeev, 28, was hit in the first minute of the Group G clash at the Gradski Stadion and was taken off on a stretcher and then substituted.
After a 35-minute delay German referee Deniz Aytekin restarted the match.
But the game was abandoned in the second half at 0-0 after a brawl involving players and coaching staff.
Uefa says it will wait to receive reports from the delegate and referee before opening disciplinary proceedings.
The start of the second half was delayed by 18 minutes because of disturbances and fighting then broke out when Roman Shirokov's 66th-minute penalty was saved by Montenegro goalkeeper Vukasin Poleksic.
Aytekin then led the players from the pitch for a second and final time.
Montenegro, who included Manchester City striker Stevan Jovetic in their starting line-up, are currently tied on five points with Russia in the group.
CSKA Moscow's Akinfeev was struck on the head by the flare approximately 20 seconds after kick-off and was replaced by substitute goalkeeper Yuri Lodygin.
Akinfeev was taken to the local hospital in the Montenegrin capital Podgorica, wearing a neck brace.
Miljan Zindovic, an emergency care doctor at Podgorica hospital, said Akinfeev was brought to the hospital with a neck injury and minor burns.
An examination determined he had no major injuries, but the goalkeeper would remain under observation in the hospital for "a few hours" according to Zindovic.
Russia goalkeeper Igor Akinfeev was struck on the back of the head by a flare as their Euro 2016 qualifier with Montenegro in Podgorica was abandoned.