It could prove invaluable in the run-in, though Boro will have to show a dramatic improvement if they are to pull clear of the drop zone.
Marlon King, the on-loan striker from Hull City, was the saviour, but it was a bitter blow for Pompey and their 600-plus fans.
Pompey had looked set for a double after reaching a milestone in the club's history. The first-half goal by Peter Crouch was their 2,000th League goal away from Fratton Park.
The visitors had looked the more impressive side until Middlesbrough's late rally.
Portsmouth were the first to threaten and there was a lucky let-off for Middlesbrough when David Nugent hit a post following a lay-off by Crouch.
Boro struggled for a breakthrough and it was no surprise when Crouch ended a personal goal drought in the 30th minute. From a Jermaine Pennant corner on the right Crouch fired a right-foot shot past Brad Jones.
Home manager Gareth Southgate had made pre-match pleas for impassioned support but there was a subdued atmosphere around the Riverside Stadium compared to the last home game against Liverpool.
Portsmouth lost Pennant after 36 minutes and his place was taken by Nadir Belhadj.
Middlesbrough were struggling in midfield at this stage and Portsmouth, fresh from their sunshine break in Dubai, were moving the ball around better.
David James was not even troubled in the Pompey goal in the first half. The England goalkeeper did not even have a direct shot to save.
Middlesbrough fans were hoping for dramatic improvement from their team in the second half. The home side resumed without Emanuel Pogatetz, who had seemingly picked up an injury.
Boro midfielder Michael Bates was booked for a foul four minutes after the break. It did not appear serious at the time, but the player paid the penalty later in the game with his second booking.
Niko Kranjcar was not far off-target with a free-kick for Portsmouth.
Second-half substitute Andrew Taylor had a shot saved by James after 59 minutes, it was Middlesbrough's first on-target shot of the game.
After 76 minutes Boro suffered a blow when Bates received his second booking for diving and was immediately shown the red card.
The home side piled on pressure in a desperate bid to save the game and James showed his class with important saves.
He could not prevent King from scoring, but denied substitute Afonso Alves a winning goal in the final seconds.