Two trademark throw-ins from Dave Challinor helped Tranmere bounce back from Worthington Cup final heartbreak and record their first League win of the year.
Challinor flung the ball to the far post a minute from time to set up the on-rushing Steve Yates who crashed a right-foot volley past the despairing Russell Hoult.
Challinor had earlier set up defender Reuben Hazell for his first League goal and the first of the match for Rovers. His 40-yard throw was only headed to Hazell by Pompey captain Adrian Whitbread.
Hazell mis-hit his shot but the ball squeezed through a packed Portsmouth defence and past on-loan keeper Hoult.
Steve Claridge had given the South coast club hope with an equaliser seven minutes from time on the day that he was charged with misconduct by the Football Association after betting on the outcome of the home match with Barnsley in January.
The former Wolves striker was brought down by Challinor and he stepped up to take the spot-kick and send teenage Rovers keeper Joe Murphy the wrong way.
Claridge could have scored a hat-trick if he had had more luck. He should have given his side the lead after 25 minutes after being put through by Australian Mike Panopoulos.
The well-measured through-ball gave Claridge too much time and he delayed his shot before shooting against the legs of the on-rushing Murphy.
After 67 minutes Claridge headed against Murphy's left-hand post. A well delivered free-kick from Sammy Igoe was met at the near post by Claridge but the woodwork denied him.
Tranmere arrived on the South Coast just three days after their Wembley defeat by Leicester, but could have taken the lead as early as the fourth minute when Hazell crossed to the far post.
His delivery beat the Pompey back line but it also evaded the outstretched boot of striker Wayne Allison.
It would have been the perfect send off for the 31-year-old who will be away for the next fortnight on international duty with the Cayman Islands.
Pompey came close to equalising on 66 minutes but Challinor was to prevent them. The Tranmere hero headed off the line and the ball was hacked away to safety after on-loan Arsenal defender Jason Crowe had headed towards the top corner.