Pompey had to settle for a point at Morecambe after conceding a controversial goal right at the death.
The 1-1 draw in the north-west ended any lingering hopes the Blues had about sneaking into the play-offs.
Danny Cowley's side went ahead through Sean Raggett's fine finish, while Jonah Ayunga's stoppage-time leveller was allowed to stand, despite a push on Gavin Bazunu.
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