Manucho pounced deep into stoppage time to clinch a dramatic victory for Hull at Craven Cottage.
The Tigers were under siege for most of the second half until Manucho combined with fellow substitute Richard Garcia, who had been on the pitch for two minutes, to secure an unlikely three points.
Bobby Zamora, Andy Johnson, Clint Dempsey and Simon Davies should have put the Cottagers out of sight 20 minutes into the second half but failed to convert.
Hull keeper Matt Duke had a major hand in their downfall, keeping out Dempsey and Johnson with superb saves, but Zamora will have nightmares over his botched three-yard tap in.
A solitary win in their last 18 Barclays Premier League encounters had sent Hull into freefall but tonight's victory has put them five points clear of the drop zone.
Tigers boss Phil Brown, who saw Ian Ashbee, Craig Fagan and Michael Turner pass fitness tests, buried the hatchet with Geovanni by including the Brazilian in his starting line-up.
Geovanni reacted angrily at being substituted in Sunday's 2-1 defeat by Blackburn, staring aggressively at Brown and ranting as he took his seat on the bench.
He later issued an apology and Brown refused to make an example of him tonight - just as well as his key playmaker was Hull's best player on the pitch.
Fired up, Geovanni was in the thick of the early action, producing a niggly challenge on John Pantsil and then firing a free-kick a hair's breadth wide of the left post.
Fulham keeper Mark Schwarzer dealt with a looping header by former Cottagers target Daniel Cousin as Hull continued to press.
The visitors' goal came under pressure for the first time in the 12th minute when Zamora jinked his way into a shooting position only to fire wide.
An incisive run from Geovanni cut Fulham open but Bernard Mendy's ball into the box was poor, wasting the Brazilian's good work.
Davies and Paul Konchesky combined to set up a half-chance for Johnson with the little striker defying gravity to connect with the ball only for his header to sail wide.
Hull's defence was unlocked once again in the 27th minute but Johnson over-ran Zamora's pass while Dempsey saw his follow-up effort at the far post blocked.
With Davies prominent Fulham were beginning crank up the pressure on an increasingly ragged Tigers back four.
Regaining his composure after a string of dreadful touches, Zamora teed up Davies to perfection but the Wales midfielder smashed his effort into the turf and over the bar.
Johnson forced a fingertip save from Hull keeper Matt Duke seconds after the break and then it was Zamora's turn to cause panic in the visitors' defence.
He backed into Kevin Kilbane, who was all over the former West Ham marksman, and tumbled to the floor but referee Mike Jones was unimpressed by his penalty claim.
Lightening reactions from Duke then kept out a blistering drive from Dempsey and moments later Johnson was denied on the line by Mendy.
Johnson tried his luck from long range but found Duke waiting while at the other end Craig Fagan set up Cousin who blasted high.
Superb approach play created a gilt-edged chance for Zamora but amazingly he squandered a simple tap-in from three yards out.
For all Fulham's dominance the score was still level and in the final 15 minutes the balance of power began to shift.
Brede Hangeland and Dickson Etuhu were booked as the home defence began to struggle in the face of several rapid counters.
Duke kept out Dempsey and then Michael Turner tackled Johnson in the nick of time as Fulham searched in vain for a late winner.
Instead, the decisive blow came from Hull deep into injury time with Garcia picking out Manucho for the Angolan to bundle home.