The Shrimps played some neat football against the highly-fancied home side but struggled to create many clear openings as they failed to score for the fourth time in five games.
Jim Bentley’s side went a goal down on 26 minutes through a superb Dan Jones free-kick.
Michael Rose had been adjudged to have fouled Shola Ameobi just outside the Morecambe box and left back Jones stepped up to curl the ball over the wall and into the top left-hand corner of Barry Roche’s goal.
The home side had created the better of the few chances on offer before the goal with Roche producing a flying save to palm away a curling effort from former Newcastle man Ameobi while the Shrimps were also grateful to defender Aaron McGowan for a fine block from Terry Hawkridge’s shot on the left-hand side.
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Morecambe’s best opening came from a 25th minute corner when Rose found the unmarked Steven Old but he could only direct his header straight at Adam Collin.
The second half saw Morecambe again play some good passing football and they forced a string of corners in quick succession.
But again Collin remained untested in the home goal with the Shrimps’ only effort being a Garry Thompson shot on the turn that skewed well wide of the Magpies’ goal.
As the Shrimps pushed forward they left gaps at the back and Notts County took advantage with a second goal five minutes from time.
Substitute Jonathan Forte got behind McGowan for a free run on goal which ended with a perfectly placed shot to beat Roche from a tight angle.
Morecambe pressed for a late consolation goal and Collin was forced to save well from Thompson and Elliot Osborne in injury time but it was too little, too late for the Shrimps.
Notts County: Collin, Hunt (Millsom 70), Brisley, Duffy, Jones, Hawkridge, Yates, Grant (Alessandra 88), Hewitt, Stead, Ameobi (Forte 45). Subs not used: Fitzsimmons, Dickinson, Hollis, Smith.
Morecambe: Roche, McGowan, Winnard, Old, Brough, Muller, Rose (Osborne 46), Campbell, Thompson, Wildig (Ellison 67), McGurk (Lang 74). Subs not used: Nizic, Lund, Fleming, Kenyon.
Referee: Richard Clark.
Attendance: 5,305.