Yakubu, who joined Middlesbrough from Portsmouth for £7.5 million in the summer, had expressed his optimism over scoring on the eve of the game.
"I feel I am in good form. The more goals I score the greater my confidence", he said.
After going a goal behind in the opening minute of the second half Middlesbrough were grateful for a header from their leading scorer in the 54th minute.
Yakubu was at the far post to connect with a left wing corner from Fabio Rochemback.
There was some booing from the Middlesbrough fans at the final whistle but a gallant band of 150 Pompey fans were jubilant. A point was some reward for their long journey from the south coast.
Whoever planned a 5.15 pm Kick-off could have had no thought for Pompey fans who would not get home until the early hours.
Middlesbrough were the first to threaten through Massimo Maccarone when the Italian shot wide with an overhead kick.
Maccarone was an £8,000,000 flop in his first spell at the Riverside Stadium but he has won over critical fans with his enthusiasm and spirit the second time around.
Middlesbrough enjoyed the better of the attacking play in the early stages, although former Newcastle United winger Laurent Robert shot high and wide in a Pompey counter-attack.
Boro goalkeeper Mark Schwarzer, recalled after recovering from a shoulder injury, made an easy save from Zvonimir Vukic shortly after.
Despite their pressure Middlesbrough did not put visiting goalkeeper Jamie Ashdown under any serious danger.
Pompey could have snatched the lead with the best move of the first half. Robert found Andrew Griffin out on the right and from his cross Dario Silva just failed to reach the ball at the far post.
If Silva had connected it would have been a certain goal.
Middlesbrough manager Steve McClaren appeared on the touchline, urging his players forward. But they responded by starting to spread the ball around in defence rather than going flat out for a goal, prompting an angry response from the home fans.
Yakubu tried a snap shot shortly before the break, but there was no power behind it and Ashdown collected the ball without any trouble.
A section of Middlesbrough fans expressed their displeasure as the teams walked off after a disappointing first half.
The second half was barely 60 seconds old when Portsmouth took the lead. Substitute Svetoslav Todorov was involved in the move which finished with Gary O'Neil shooting into the top corner of the net.
Pompey were jubilant about their shock lead but McClaren must have been angry with the slack marking in his defence.
It did not take long for Middlesbrough to draw level and there was an air of inevitability about Yakubu scoring the goal.
Immediately McClaren tried a double substitute by sending on experienced international strikers Mark Viduka and Jimmy Hasselbank.
Boro now had three big guns in attack in a gamble to win the game.
Portsmouth brought on Gregory Vignal for Robert. The temperamental winger did not look happy as he trudged off the field but the move was designed to tighten the defence.
There was more urgency about Middlesbrough's play at this stage and Viduka tried a shot from an acute angle. There was plenty of power behind his shot but Ashdown was well positioned to save.
Substitute Gaizka Mendieta found the unmarked Yakubu with a brilliant pass but the striker shot wide when challenged by Ashdown.
Middlesbrough piled on pressure but there was no sign of panic from Portsmouth. They played the ball out of defence calmly without resorting to the big boot.
The point will give them encouragement in their battle to hold on to Premiership status.
Man of the Match: Gary O'Neil
Apart from scoring a vital goal, O'Neil was prominent throughout with his intelligent runs from midfield.