Brnovic, who replaced Zlatko Kranjcar as coach following September's defeat by Wales, said Milan Jovanovic, Nikola Drincic and Marko Basa would not play in Friday's clash in Podgorica, along with the injured Mitar Novakovic.
Montenegro could still beat England to top spot and automatic qualification for the tournament in Poland and Ukraine.
Brnovic knows, however, that victory in Friday's match would not be enough to seal second place and a two-legged qualification play-off unless Switzerland, who are also chasing the runners-up spot, failed to beat Wales.
"If I knew that Wales were going to beat Switzerland, I would field my strongest team," Brnovic told a news conference on Thursday.
"However we have eight players on one yellow card and we have to reduce the risk.
"If we were complete, I am sure that we would win, but I still do believe in this team.
"Unfortunately, we do have to think about next game."
Montenegro, who first played as an independent nation in the 2010 World Cup qualifiers, are six points behind England in second having played one match fewer. Switzerland are third and three points further adrift.
Montenegro captain Mirko Vucinic said cool heads would be required if they are to prevail on Friday.
"Our motive is huge, but we have to control our emotions. We are not afraid of anybody, and we will try to win," he said.
"Who knows when we might be in this situation again to go on such huge competition."
