Needing only a point to guarantee top spot in the group, goals by Ashley Young and Darren Bent had Fabio Capello's side in cruise control after 31 minutes on a rainy night in the Balkans before things became unexpectedly more complicated.
First Elsad Zverotic volleyed a reply with the final kick of the first half and in a frantic finale substitute Andrija Delibasic headed a dramatic equaliser to guarantee Montenegro second place and a play-off spot in the fledgling nation's first tournament campaign.
Rooney, who had been involved in both England goals, received a straight red card for a petulant kick on Miodrag Dzudovic with a little under 20 minutes remaining and will miss the start of next year's finals in Poland and Ukraine.
The Manchester United striker, who suffered the second red card of his England career, could even face a three-match ban which would have serious implications for England's chances of success next year.
England ended with 18 points ahead of Montenegro on 12. Switzerland, who host Montenegro on Tuesday, can no longer secure a play-off place after defeat in Wales.
"We are a little bit disappointed because we were 2-0 up and ended up drawing the game," captain John Terry told Sky Sports. "But it's a great feeling to get where we've got and we're top of the group.
"We were really in control and the manager said at halftime it was probably too easy for us. Wayne had a bit of a tussle, it was one of those things. Fortunately it did not cost us."
Capello said Rooney deserved to be dismissed.
"I was surprised because it was just in front of me that he kicked the opponent. I think the red card for Rooney was right," Capello said.
"The player is frustrated from [what happened] on the pitch not from what happened away from it," added the coach, referring to Rooney's father and uncle being arrested on Thursday and bailed by police over an alleged betting scam.
It was all too easy for England in the early stages and it was no surprise when Young gave the visitors the lead after 11 minutes. Rooney fed Theo Walcott and his inviting cross was tucked away by the unmarked Young.
It was 2-0 when Montenegro lost the ball in midfield and Rooney played in Young who slid a precise pass across the area for Darren Bent to tap in a goal of pure simplicity.
Montenegro had hardly offered their fans anything to shout about but they were given hope on the stroke of half-time when Zverotic's volley deflected in at the near post.
From that moment on the atmosphere inside the stadium was electric and not just because of the thunderclaps echoing around the Podgorica City Stadium as a storm moved in.
Montenegro, who began the night knowing victories in their last two games would guarantee first place in the group, began to play with much more purpose.
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