The clinching penalty was left to Vedran Corluka, who rifled past Heinze before being predictably mobbed by his team-mates.
City still created the best chance of the first half, however, and Corluka will be kicking himself for missing it.
And Pompey had another escape when Aaron Mokoena diverted Corluka's cross towards his own goal, only to recover as Crouch closed in.
James, who had stood firm, then blocked Corluka from point-blank range before Pompey broke again to score the second and decisive goal.
The 21-year-old is Eriksson's fourth signing in two days after deals for Javier Garrido, Vedran Corluka and Elano were completed on Thursday.
His bustling style caused problems for the City backline, and Croatian right-back Vedran Corluka had to make an athletic block from a Scharner effort.
Croatia full-back Corluka left the field on a stretcher and was later seen on the substitutes' bench with crutches and an ice pack on his ankle.
At the other end, Vedran Corluka and Modric combined to tee up Defoe but the England striker was denied from close range by the excellent Green.
Tottenham do, however, have a host of injury worries, with the likes of Tom Huddlestone, Michael Dawson, Ledley King, Vedran Corluka and Robbie Keane ruled out.
City's defence was stretched when Corluka had to block Doyle's ferocious shot and, from the resulting corner, Hart had to push Bikey's shot on to the bar.
Ramos has also spent big on Luka Modric, David Bentley, Roman Pavlyuchenko and Vedran Corluka while losing the services of strike duo Robbie Keane and Dimitar Berbatov.
Vedran Corluka, who played at right-back on Sunday, is cup-tied for the club's Uefa Cup trip to Nijmegen on Thursday, while skipper Ledley King will be rested.
Fulham enjoyed the better early as Danny Murphy had a shot from the edge of the box blocked by Vedran Corluka and Johnson blazed over from 12 yards.
Aiden McGeady's wickedly inswinging free-kick from the left caught Vedran Corluka cold at the back post, as Sean St Ledger sneaked in to head past Croatia keeper Stipe Pletikosa.
But the Newport-born player has only played a bit-part role for Tottenham, as Gunter is one of four top-class right-backs that include Pascal Chimbonda, Alan Hutton and Vedran Corluka.
City's Vedran Corluka ghosted into space and lashed a 25-yard drive narrowly wide on 10 minutes, while Vassell saw a deft flick-on whistle wide from a Martin Petrov free-kick.
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Gattuso and 59-year-old Scot Jordan had already clashed on the touchline during a bad-tempered second half in which Mathieu Flamini escaped with a only booking for a two-footed challenge on Vedran Corluka.
As Spurs threw men forward in desperation, the excellent David James made a crucial block from Vedran Corluka before victory was sealed in front of Portsmouth's ecstatic fans three minutes from time.
The first spot-kick was given in the fourth minute after Jussi Jaaskelainen parried Michael Dawson's header straight to Vedran Corluka, whose prod towards goal was stopped by the arm of Kevin Davies.
In the trio's absence, Dorian Dervite could get a chance to impress - the 20-year-old made his only competitive start in November 2006 - while Vedran Corluka and Tom Huddlestone can also play at centre-back.
Within minutes, Jelavic just failed to climb high enough to connect with a cross from fellow substitute Ivan Perisic and Croatia were furious when Vedran Corluka appeared to have his shirt pulled in the penalty area, only for the offence to go unseen.
Flamini, jeered roundly for the twin crimes of previously playing for Arsenal and for his horror tackle on Vedran Corluka in the first leg, almost silenced the taunts with a low drive that flew inches wide with no colleague able to apply the final touch.
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