The Manchester United forward was red-carded for a second time in an England jersey for stupidly kicking Miodrag Dzudovic off the ball on 72 minutes with his team leading 2-1 through goals from Ashley Young and Darren Bent.
After Elsad Zverotic had reduced the deficit just before half-time, Montenegro netted the equaliser they needed to secure the play-off spot from Group G ahead of Switzerland when Andrija Delibasic rose to head home in the first minute of three added on for stoppages.
Rooney will serve his ban at the Euro 2012 finals. UEFA have confirmed he is in line for a one-match suspension, but it could yet be a more severe punishment for the player depending on how German referee Wolfgang Stark viewed it.
Needing only a point to secure qualification, Fabio Capello’s side made a vibrant start to the evening in their final match of the section.
They secured a deserved lead when Theo Walcott crossed deep for Young to nod home at the back post from close range on 11 minutes.
They added a second when Bent popped up on 31 minutes to nudge the ball over the line for his fourth England goal after Young had delivered a timely cross from Rooney’s delightful pass.
Montenegro had offered little in the first period, but somehow gave themselves hope when Zverotic saw a deflected shot spin off the foot off Gary Cahill from Fatos Beciraj's cross before beating a sprawling Joe Hart in the England goal on 44 minutes.
It was a real Jekyll and Hyde performance from England and from Rooney, who enjoyed an outstanding opening 45 minutes before appearing to take leave of his senses in the second half with his team handily placed to sign off with a win in Capello's final qualifying contest.
England had kept the ball impressively until the home side struck moments before half-time. They were fortunate not to concede a penalty when Phil Jones appeared to fell Stevan Jovetic in the area only for referee Stark to wave play on.
Joe Hart was forced to swat Milorad Pekovic’s shot behind a post with 15 minutes remaining as Montenegro began to load the visiting area with bodies against the 10 men.
Jovetic was booked for an outrageous dive in the visiting box as the rain continued to lash down with two minutes left before England finally buckled when Delibasic rose highest from Stefan Savic’s cross to power the ball into the net for the goal a young nation craved.
The goal prompted wild celebrations among the home crowd with Delibasic booked for rushing off to celebrate with a vociferous bunch of supporters.
Switzerland's 2-0 loss in Wales means Montenegro are assured of second spot in the section, holding a four-point lead before they visit the Swiss in their final match of the group on Tuesday night.
England win the group with 18 points from eight games with Montenegro moving on to 12 points from seven outings.
But the sense of joy Capello will feel at steering England to the finals in Poland and Ukraine will be tempered by the news that Rooney will watch England's opening match at the tournament from the stands.
He must hope UEFA do not dole out further punishment to Rooney - who was previously sent off during England's defeat to Portugal in the 2006 World Cup quarter-finals for stamping on Ricardo Carvalho - in the coming days.