Russia goalkeeper Igor Akinfeev was struck by a flare and Dmitri Kombarov apparently by a coin, the latter incident leading to the clash being called off in the 67th minute with the score at 0-0 in Podgorica.
Montenegro sit fourth in Group G, level on points with Russia, with UEFA set to investigate the incidents at the Stadion pod Goricom.
Brnovic said the game would rightly be questioned in Montenegro.
"We left a very bad image," he told RTCG.
"It's a shame, I feel sorry for the players, now we definitely not only have no chance of qualifying, but the question is what will happen with football in Montenegro?
"The situation is difficult, for all of us, but certainly for football in Montenegro."
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