Morison clinched the points four minutes after the break as he dispossessed defender Adam Virgo before rounding goalkeeper Michel Kuipers and planting the ball into an empty net.
Brighton rarely threatened on a difficult, bobbly pitch, although veteran striker Nicky Forster almost hit back immediately after Morison's goal but fired narrowly over.
Seagulls defender Tommy Elphick had a header cleared off the line late on and Glenn Murray also saw an effort rebound off a post.
Millwall striker Shaun Batt was twice denied by Kuipers as the Lions threatened on the counter-attack.
Kuipers saved an early shot from Chris Hackett before Elliott Bennett put a powerful free-kick just wide for Brighton. Brighton skipper Andrew Crofts went close with a fierce 20-yard drive which flew just over the crossbar in the 25th minute.