Due to Bolton Wanderers confirming their position in third spot thanks to a win against Crawley Town, goals from Liam McAlinden and Cole Stockton were not enough to lift the Shrimpers into the promotion places.
Derek Adams will however be able to take confidence into the upcoming League Two play-offs after a commanding display against a Bradford side who now end their season with a sixth defeat in seven games.
Story of the match
Morecambe began the game knowing they would require taking at least a point if they were to have any chance of securing automatic promotion regardless of results elsewhere and they made an attacking start to the match, coming within inches of taking an early lead when Bradford goalkeeper Sam Hornby made an impressive save to deny a close range shot from Brad Lyons but could only parry the ball into the path of forward Liam McAlinden, who then saw his effort slam back off the post with 16 minutes gone.
The Shrimpers again came close just minutes later when full-back Ryan Cooney let fly from 20 yards before seeing his well struck effort bounce narrowly wide of the post.
The promotion chasers did not have to wait long for their eventual opener however, with McAlinden putting his side ahead after 28 minutes after being expertly played in behind the Bantams defence by Toumani Diagouraga, before calmly finishing into the bottom corner.
Despite enjoying the majority of the possession, Bradford struggled to create any clear cut chances and once again came close to conceding shortly after half time when Ryan Cooney played a dangerous ball into the penalty area which fell into the path Diagouraga, whose powerful volley flew just wide of the City goal.
The Lancashire side did eventually double their lead just seven minutes later though, when Carlos Mendes Gomes played a pinpoint ball into the box for fellow striker Cole Stockton who swept convincingly past Hornby in the Bradford goal.
Bantams coaches Mark Sellers and Connor Truman did make a number of attacking changes in an attempt to salvage a result from the game, including bringing on veteran attackers Clayton Donaldson and Billy Clarke, but they struggled to create chances, coming closest to grabbing a goal in the 94th minute when Shrimps 'keeper Kyle Letheren produced a quick reflex save to deny a close range header from Clarke after getting on the end of a good cross from Callum Cooke.
Morecambe were able to comfortably hold on for the victory but due to Bolton's win against Crawley, the three points were not enough to allow them to climb into the top three, as a result they will enter the play-off's and finish their season in fourth place.
Bradford on the other hand, drop one place in the table and end what has been a very mixed campaign for the West Yorkshire club in 15th spot.
Man of the match - Liam McAlinden
The 27-year-old produced a memorable performance to cap off what has been a promising season for him.
His opening goal took the edge of what could have ended up being a frustrating afternoon for the Shrimpers and he could count himself unlucky not to have added further to his goal tally throughout the match.
McAlinden also largely ran the show for Morecambe in the middle of the park, and managed to help create good goal scoring opportunities for his team mates on a number of occasions.