WAFCON: Ghana set up last eight clash with Fazili's Malawian debutants
Evelyn Badu scored the opener at the Stade Moulay Rachid in Casablanca just before half-time on Thursday night.
Kadidiatou Diabaté levelled just after the restart but Mali failed to breach the Ghana rearguard again for the strike that would have taken them into the last eight.
"Going through to the last eight was one of our targets," said Ghana boss Kim Björkegren.
"It was our best game of the tournament and the only thing I can be disappointed about is that we were nervous at the end and we should have closed the game way earlier.
"We played really good football and I think we were ready from the start. We needed one point and we took it and we're into the quarter-finals."
'Extraordinary performance'
In the last eight, Ghana will face a Malawi side that topped a pool that included defending champions Nigeria as well as tournament stalwarts Zambia.
"I think it's extraordinary that we've qualified for the last eight," said Malawi boss Lovemore Fazili.
"Especially where we're coming from ... but given the way we were playing in the group stages, it has been good.
"We were playing tough teams and finishing top of the group is excellent."
Malawi will take on the Ghanaians at the Stade Al Medina in Rabat after Nigeria continue the defence of their crown againstCameroon at the Stade Larbi Zaouli in Casablanca.
In Saturday's quarter-finals, hosts Morocco play South Africa at the Stade Moulay El Hassan in Rabat and Cote d'Ivoire face Algeria at the Stade Moulay Rachid in Casablanca.
The four sides who reach the semi-finals also claim a berth at the 2027 Women's World Cup in Brazil, while the four losing teams will head to a play-off for two spots at an inter-confederation qualifier.