Jed Wallace's well-taken 15th minute goal and a late Patrick Agyemang header were enough to condemn the Sky Blues to a first away defeat since January 13.
It came 48 hours after owners SISU placed a subsidiary company into administration, leaving them facing a 10-point deduction, all but ending their play-off hopes.
Coventry could have taken the lead after only seven minutes when they were awarded a penalty after Cody McDonald was bundled over by Pompey midfielder Shaun Cooper.
Home goalkeeper Simon Eastwood spared Cooper's blushes by producing an excellent save to keep out Gary McSheffrey's spot kick.
McSheffrey's misery was compounded when Wallace fired the hosts in front from six yards after combining neatly with Cooper.
Coventry improved after half-time and were thwarted by a number of fine saves from Eastwood.
But Agyemang secured the points for Pompey 14 minutes from time, rising above the Coventry defence to flick Liam Walker's cross beyond Joe Murphy.