Spurs made a switch at half-time, with former Liverpool midfield man Danny Murphy coming on for Teemu Tainio.
Danny Murphy converted the penalty and Zamora laid in Seol Ki-Hyeon, who smashed home a third late on.
But Danny Murphy's penalty drew Fulham level early in the second half before Zoltan Gera put the visitors ahead.
Fulham captain Danny Murphy pulled one back from the spot in the 75th minute but they could not force an equalizer.
Midfielder Danny Murphy started to move further forward and Gera and Carlos Salcido attempted shots, though both failed to trouble Howard.
Danny Murphy struck the decisive goal in the 57th minute, driving home Andrew Johnson's superb pull-back for his third goal of the season.
Danny Murphy went close for Cork on 32 minutes and Joe Gamble then wasted the best first-half chance when he pulled a snapshot wide.
Danny Murphy equalised nine minutes later, slotting home after Joe hart saved his penalty, and Kamara fired the winner in the very last minute.
Farren had a late chance as Derry pressed in the closing minutes but he delayed his shot and Danny Murphy got back to make a vital block.
Shortly after, he held up a pass from Danny Murphy with his back to goal in the box before teeing up Duff to slam home from 12 yards.
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.
Hodgson has harnessed the composure of veteran Danny Murphy in midfield and this, coupled with the return from injury of key duo Jimmy Bullard and Brian McBride, has proved the catalyst for recovery.
Danny Murphy split two defenders with a pass to the edge of the box to Zamora and after his cute lay-off, Gera lashed under the body of Pyatov from an angle on the left.
Fulham might have reduced the deficit before the break as a decent Simon Davies run ended in a chance for Danny Murphy, but he steered his shot over from the edge of the box.
Danny Murphy's free-kick was met by Heskey's head as he muscled his way into the penalty area, but he was only able to direct his effort straight at Seaman, who pushed it to safety.
It was a match where the result outweighed the manner of performance with Fulham manager Roy Hodgson travelling to eastern Europe without Danny Murphy, Bobby Zamora and Paul Konchesky, as well as striker Andy Johnson.
Danny Murphy's chip found Simon Davies on the edge of the area and he was able to turn and fire a shot that found its way through defender John Thompson's legs and past goalkeeper Kasper Schmeichel.
He not only rejuvenated the likes of Danny Murphy and Simon Davies, but identified unheralded talents such as Brede Hangeland and experienced players who had fallen out of favour at their previous clubs - Mark Schwarzer, Zoltan Gera, Bobby Zamora and Damien Duff to name but four.
Hodgson's carefully crafted team of budget signings (Zoltan Gera, a free transfer from West Brom), obscure European finds (Brede Hangeland from FC Copenhagen) and rejuvenated 'Big Four' cast-offs (Danny Murphy, ex-Liverpool, and former Chelsea winger Damien Duff) have negotiated 14 games on their way to their maiden European final.
With Eddie Murphy, as a desperate soul singer loosely based on James Brown, and Danny Glover, as an aging business manager.
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