The game seemed destined for a frustrating stalemate from the Sky Blues' perspective, but Jamie Paterson had other ideas.
Paterson struck a high-class winner, volleying home in the fourth minute of added time as Coventry went above Middlesbrough and into sixth spot.
"We didn't play at our best, Portsmouth didn't allow us to, but we showed incredible character to push in the second half and got what we deserved," Coventry manager Frank Lampard said.
"You score a goal, the fans erupt and the players are excited and their fans are distraught. We had it at Norwich so I feel for them tonight."
Former Brisbane Roar striker Thomas Waddingham played 55 minutes before being substituted for Pompey, who remain 17th and just three points above the relegation zone.
"93 minutes and 50 seconds of really good football and 10 seconds of madness," a disappointed Portsmouth boss John Mousinho said.
Bottom club Plymouth Argyle remain three points adrift at the basement with just five games left following a 3-0 defeat at Swansea City.
All the damage was done during an opening 45 minutes on Wednesday night when Swansea had complete control, never looking back after Lewis O'Brien gave them an early lead before Harry Darling scored the second and Josh Key added a third.
Swans' caretaker manager Alan Sheehan has now collected 14 points from eight league games since taking the reins following the departure of Luke Williams in February.
Oxford United were left just three points above the drop zone after Queens Park Rangers beat them 3-1 at the Kassam Stadium.
Ronnie Edwards put QPR ahead in the seventh minute, before their advantage was doubled just before the interval through an Ole Romeny own goal.
Stanley Mills pulled a goal back for Oxford midway through the second half, but Yang Min-hyeok made certain of maximum points with a left-footed shot in added time.
With AAP.
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