A late fightback could not prevent Fleetwood losing their eighth game in a row as Portsmouth became the latest team to collect three points Highbury.
The sacking of manager Uwe Rosler failed to reverse Town's fortunes as Saturday's 3-0 loss to Doncaster was followed by a 2-1 reverse.
They fell behind to a 24th-minute strike from Jamal Lowe, who curled home after Ben Close's shot was blocked.
Caretaker head coach Barry Nicholson's first taste of the hot-seat in league football did not go to plan, with Oliver Hawkins giving the visitors a 2-0 lead in the 75th minute as he bundled home Lowe's parried cross.
The hosts did show some spirit late on as a superb Conor McAleny strike in the 82nd minute set up a tense finish.
Fleetwood dominated the dying embers but they could not find that elusive leveller and remain just above the drop zone.