Australian Tim Cahill headed home the winner ten minutes from time as Everton's remarkable change in fortunes continued as they maintained their best ever start to a Premiership season on the South Coast.
Cahill produced the decisive moment of a hard-fought game on 80 minutes when he beat his marker Andy Griffin to head home Lee Carsley's free kick at the far post giving goalkeeper Shaka Hislop no chance.
Everton have now won three out of their four away games this season to lie just three points behind Arsenal and they have not lost since the opening day of the season when they were beaten 4-1 at home by the Gunners.
Cahill, a £2million signing from Millwall in the summer, was the only big money signing that manager David Moyes made during a close season which saw a string of departures from Goodison Park including England star Wayne Rooney.
But the midfielder showed he has already developed the happy knack of scoring crucial goals when he headed home from eight yards to hand Portsmouth their first home defeat in six months.
Harry Redknapp's Pompey side had last lost at home against Arsenal in the FA Cup in March but they found themselves outbattled and second best for large periods of the game and could easily have gone behind before Cahill produced the crucial moment.
Portsmouth made the better start and both sides could easily have opened their goal accounts within the space of 90 seconds as play opened up.
Nigel Quashie's hopeful shot in the 12th minute was deflected goalwards by team-mate Eyal Berkovic and it needed a sprawling save from Everton's Nigel Martyn to tip the ball around the post for a corner.
The action immediately switched to the other end with Steve Watson hitting the outside of the left-hand upright with a first-time volley from Alessandro Pistone's cross from the left while Quashie was unlucky to see a 25-yard shot cannon off the woodwork to safety just a minute later.
Everton grew in confidence as the half progressed with Portsmouth frequently finding themselves on the back foot.
Home midfielder Amdy Faye should have done better on the half-hour mark when he volleyed wide when unmarked eight yards out but it was the visitors who looked more dangerous with Thomas Gravesen and striker Marcus Bent impressing in their attack.
Portsmouth defender Dejan Stefanovic somehow scrambled the ball away from Bent's heels on the goal-line in the 20th minute while it took a fine clearing header from David Unsworth, making his first appearance against his former club since a summer move, to deny Cahill after being set up by Bent four minutes before the break.
Portsmouth's goal continued to find itself under pressure after the interval and the introduction of giant Scottish striker Duncan Ferguson only served to increase their anguish and anxiety at the back.