Local hero Stewart Downing rescued a point for Middlesbrough with an equaliser 16 minutes from full-time.
Downing has become a crowd favourite at the Riverside this season after progressing through the club's Academy.
A tricky winger, Downing has already been tipped to solve England's left-sided problem position in the future.
Manager Steve McClaren is keen to protect a player who has been labelled 'boy wonder' following recent displays.
McClaren insisted that Downing has a long way to go, but if he continues to improve the England Under-21 International looks certain to win recognition at senior level.
The loss of two home points was a blow to Middlesbrough's hopes of a top-six finish at the end of the season.
Portsmouth shook Boro when they opened the scoring through Diomansy Kamara after five minutes.
Kamara burst through the middle and rounded his run off with a brilliant effort that left keeper Mark Schwarzer helpless.
Kamara celebrated by taking off his shirt and was promptly booked by the referee.
This was a setback to Middlesbrough's hopes of avenging a 5-1 drubbing at Fratton Park at the end of last season.
Pompey played with speed and confidence in the first half, with no intention of putting up the defensive shutters.
Jimmy Floyd Hasselbaink, who scored a hat-trick in a 4-0 win at Blackburn Rovers, was a real threat for the home side.
His partner, Mark Viduka, however struggled to make an impression, but it was clear the former Leeds United striker is well short of match fitness after a hip injury.
Portsmouth keeper Shaka Hislop denied Boro on several occasions before a brilliant last-ditch tackle by Anthony McMahon denied Kamara as he burst through after 34 minutes.
Two minutes later Middlesbrough midfielder Gaizka Mendieta was hurt and stretchered off to be replaced by Szilard Nemeth.
With Ray Parlour working tirelessly in midfield, Middlesbrough stepped up the pressure and nearly snatched an equaliser on the stroke of half-time, when a Nemeth header was cleared off the goal line by Yakubu with Hislop beaten.
For the second half Portsmouth brought on substitute Matthew Taylor for David Unsworth.
Middlesbrough piled on the pressure to pull the game round but Pompey showed plenty of fighting spirit.
Boro tried hard to unlock the Portsmouth defence, with Hislop in almost constant action, and it was perhaps inevitable that Middlesbrough would achieve a breakthrough.
Downing had switched to the right wing and the move paid dividends when he ran towards the penalty area and shot past Hislop.
It was also perhaps inevitable that Middlesbrough fans gave out a 'Downing for England' chant.
Viduka came close to becoming a match winning hero. Six minutes from time his header was pushed onto a post by Hislop.
In the final minute Portsmouth substitute Ricardo Fuller was booked for a foul on George Boateng, who limped off the field to be replaced by veteran Colin Cooper.
Middlesbrough's territorial supremacy was summed up by the fact that they had 21 goal attempts, compared to Pompey's three.
Portsmouth, however, won credit from their fans for a never-say-die spirit.
The Pompey fans deserved credit too, for their constant support after a 300-mile trip to the north east.