The Saturday win earned at the Mohammed V Stadium makes Morocco the second North African side to sail through to the 2013 AFCON to be played in South Africa from 9 January next year.
Earlier on Saturday, Tunisia needed the away goals rule to qualify with a 2-2 aggregate win over Sierra Leone after the two tied 0-0 in the reverse tie played in Tunisia at the 7 Novembre Stadium.
Mozambique did well to hold Morocco who led at the break 1-0. At that point, the Mambas were ahead 2-1 on aggregate.
But the game had a turn around three minutes after the hour mark when Mozambique defender Daniel Almiro Lobo aka Miro of South African side Platinum Stars was slapped with a straight red card.
A man less, Mozambique then conceded three goals thereafter; from a Houssine Kharja penalty on 64 minutes, Youssef El Arabi and Nordin Amrabat goals on 85 and 90 minutes.
Morocco’s first half goal was scored on 39 minutes through Abdelaziz Barrada.
Ivory Coast is as good as through as the team leads Senegal 6-2 on aggregate. Their reverse tie at Senegal on Saturday was abandoned with less than ten minutes to go with Senegal 0-2 down to a Didier Drogba brace.