Early goals looked set to seal a comfortable night for the Three Lions, but a goal on the stroke of half-time and a sending off made for a nervy finish after the host's late strike
The visitors had led through early goals from Ashley Young and Darren Bent, but were pegged back just before half-time.
However, the Manchester United striker received a needless sending off that will rule him out of the opening of Euro 2012, before Montenegro picked up a late equaliser.
Phil Jones, making his England debut, almost opened the scoring in the third minute, taking on two players before firing in a cross that popped out of Mladen Bozovic's hands and over the bar.
Bozovic was in action again soon after, awkwardly getting down to block a Theo Walcott volley from the edge of the area following a bright start from the visitors.
Montenegro did threaten in and around the area, but lacked the end product that was produced in the 10th minute as Rooney found Walcott in acres of space on the right-wing, who quite brilliantly found Young at the far post to nod home.
The game slowed to near walking pace over the course of the next 20 minutes, with Fabio Capello clearly angered at his team's decrease in tempo. But on the half hour mark, England increased their lead and seemed to have all-but sealed qualification for next year's finals.
Gareth Barry won the ball in midfield and shifted it to Scott Parker, who found Rooney in space in the centre of the pitch. The striker then slid the ball into Young with a perfectly weighted pass, before the winger squared for Bent to finish.
It was a devastating counter attack from the Three Lions, and the simplicity of both goals underlined the lack of quality in the Montenegro defence.
But right on the stroke of half-time, Montenegro halved the deficit as Elsad Zverotic found himself in far too much space in the area as he chested down and volleyed the ball towards goal, as it took a deflection off Gary Cahill's foot and into the corner of the net with Joe Hart helpless.
Five minutes into the second half, the debutant Jones was a relieved man after he challenged clumsily in the box.
Wayne Looney | Striker receives needless red card to rule him out of start of Euro 2012
The Manchester United defender got on the wrong-side of Stevan Jovetic, and appeared to bring him down, though the referee pointed only for a goal-kick when a penalty looked the likely outcome.
A lot of the second half progressed without note, as the sides became bogged down in a midfield battle, with Parker and Barry effectively shielding the defence.
The flow of the game wasn't helped by Capello introducing a third central midfielder into an already crowded section, as Bent and Young made way for Frank Lampard and Stewart Downing.
And in the 73rd minute, Rooney took out his frustrations at becoming a marginal figure on the match by swinging a boot in anger in the direction of Dzudovic, giving the referee no option but to brandish the red card.
It was a reaction his team-mates will not thank him for, given that they were forced to see out the rest of the game a man down, and Rooney himself will pay the price of missing the opening of next summer's final tournament.
With five minutes to go Hart was called into action, making a fine stop to push the ball around the post. And immediately after England fans' hearts were in mouths, as Jovetic played a clever one-two before going down in the area under pressure from John Terry.
The referee, however, saw that it was the slightest of touches from Terry, and produced a yellow card for simulation.
But following continued pressure on the England goal, Montenegro drew level in the 91st minute as Savic's cross from the right went deep to the far post where Joe Hart could not reach, and was headed in by Andrija Delibasic to earn the hosts a draw.