Russia's match at Montenegro was abandoned in the 67th minute after the referee stopped play following a second crowd disturbance.
The game was temporarily suspended shortly after kick-off when Russian goalkeeper Igor Akinfeev appeared to be struck by a flare fired from the stands.
Play resumed after about 35 minutes, and the game was still scoreless in the 67th minute when Roman Shirokov's penalty was saved by Montenegro goalkeeper Vukasin Poleksic.
The ball went out on the sideline, and when a Russia player went to retrieve it he appeared to be hit by a thrown object, which he showed to referee Deniz Aytekin, who stopped the match a second time.
The match was officially abandoned a few minutes later. A statement on the European organising body's website read: "UEFA will wait to receive reports from the delegate and referee to open disciplinary proceedings."
Akinfeev was taken to the local hospital in the Montenegrin capital Podgorica, where he was seen on a stretcher and wearing a neck brace. UEFA doctor Slobo Mandic went with Akinfeev and said the goalkeeper was conscious.
"I hope he will be fine," Mandic said, adding that the brace was put on as a precaution.
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," Zindovic said.
Aytekin ordered the players to leave the pitch in Podgorica after the first incident, though the game resumed after a delay of about 35 minutes. Yury Lodygin replaced Akinfeev in goal for Russia.
Police arrested the Montenegro fan who threw the flare, TASS news agency reported. The stadium announcer said the match would be abandoned if any more crowd trouble occurred, and that promise was eventually fulfilled in the second half.
Akinfeev, 28, is Russia's first-choice goalkeeper and started at the World Cup in Brazil last summer. During Russia's match against Algeria, Akinfeev was the target of a laser light shining in his eyes.
Russia are third in their European qualifying group with five points in four games, just ahead of Montenegro on goal difference. The teams need to finish second to guarantee qualification to Euro 2016 in France.
It is not the first case of severe crowd trouble during a Euro 2016 qualifier. Last year, a match between Serbia and Albania was abandoned after a drone carrying a political banner was flown into the stadium.
A Serbia player pulled the banner down and Albanian players tried to protect it. In the resulting disorder, Serbian fans attacked Albania players. Both teams were punished over the incident.
Information from The Associated Press was used in this report.