Senegal striker Diomansy Kamara scored his third goal in four starts as Portsmouth booked their place in the last 16 of the Carling Cup for the second season in a row.
Kamara followed up his first Premiership goal at Middlesborough on Sunday with a superb solo effort to put Portsmouth into the lead in the 14th minute.
The former Modena star, who also hit the winner at Tranmere in the last round, was unlucky not to open the scoring as early as the second minute.
Kamara danced his way past Leeds midfielder Matt Spring before unleashing a fierce right-foot drive, which was beaten away at the post by Leeds goalkeeper Neil Sullivan.
The former Scotland shot-stopper then produced a fine one-handed save to turn Andy Griffin's long-range effort over the bar five minutes later.
Sullivan was powerless to prevent Kamara opening the scoring, when the striker took the ball the past two Leeds defenders before calming rounding the keeper and firing home from close range.
Portsmouth doubled their lead thanks to an Eyal Berkovic penalty 18 minutes later. Valery Mezague was tripped by Gary Kelly two yards inside the box and Berkovic stepped up to send Sullivan the wrong way and drive the resulting spot-kick into the bottom left-hand corner.
Striker Brian Deane pulled Leeds back into the match with a trademark header six minutes before the interval.
Kelly atoned for his penalty error by crossing from the right for Deane to plant a bullet header past Portsmouth goalkeeper Jamie Ashdown from 12 yards out.
Aliou Cisse squandered a great chance to make the game safe for Pompey shortly after the break when he fired straight at the keeper following good work from Kamara.
Deane then saw a second effort ruled out for offside after the break and Frazer Richardson fired a 25-yard curler just wide as the Whites searched for an equaliser.
Pompey boss Harry Redknapp sent on Patrik Berger and the Czech Republic international took control of the game in the closing stages.
He should have netted in the final minute only to mis-hit his shot, but it mattered little as the Premiership team held on to win.
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