Second-half goals from Gary McSheffrey and Oliver Norwood boosted Coventry's Championship survival hopes while pushing Portsmouth closer to the drop.
McSheffrey side-footed home from 12 yards before Norwood found the top corner to make the points safe.
The visitors' best chance came when Chris Maguire crashed a free-kick against the post from 20 yards.
Coventry remain in the relegation zone, only a point from safety, while Pompey are six adrift with eight to play.
The win sees the Sky Blues end a run of four successive draws, as Michael Appleton's Portsmouth failed to build on the midweek 4-1 win over Birmingham.
Before that, Pompey had gone nine games without a win.
The away side had the better of a first half that included chances for both sides.
Chris Maguire twice tested Coventry goalkeeper Joe Murphy, and Luke Varney headed Greg Halford's cross over from close range.
At the other end, Sammy Clingan's free-kick was parried by Jamie Ashdown, who produced an excellent save to deny Clive Platt.
Pompey continued in the ascendancy after the break, Joel Ward's 20-yard strike testing Murphy.
But it was City who broke the deadlock, McSheffrey finishing when Chris Hussey's scuffed shot fell at his feet.
But despite Portsmouth maintaining possession, and Maguire rattling the woodwork, it was Norwood who settled it from six yards out.