Samp were in no mood to do their city rivals any favours in their battle to beat the drop and Eder's improvised free-kick put Delio Rossi's men on course to follow up November's 3-1 derby victory and push Genoa closer to relegation.
But Matuzalem pounced on a mistake from Samp goalkeeper Sergio Romero, after Andrea Costa had seen red, to keep the Rossoblu within two points of 17th-placed Siena with six games remaining.
This was the fixture that saw Samp relegated to Serie B two years ago and the Blucerchiati were in a vengeful mood from the first whistle.
First, Mauro Icardi tumbled in the box just before turning an Andrea Poli cross home, then Marcelo Estigarribia drove just wide having skipped past two Genoa defenders.
Samp made the breakthrough midway through the first half, though, as Eder found a way through in unusual fashion with 28 minutes played.
Icardi won a free-kick from Juraj Kucka in an interesting position, Eder rolled his shot underneath the jumping wall as an unsighted Sebastian Frey watched helplessly as the ball trickled in off a post.
Genoa were slow to react and, although they tightened up a worringly porous defence, neither Ciro Immobile or Marco Borriello could find a way through before half-time.
Grifone boss Davide Ballardini responded by pushing Juan Vargas up to form a trident for the second half, but that failed to stop the dangerous Icardi, who whipped a fierce drive into the crowd in the 52nd minute.
Genoa continued to toil and Antonio Floro Flores' weak free-kick at Sergio Romero gave Rossoblu fans little reason to cheer until Matuzalem inspired them to believe again in the 80th minute.
Moments after Costa's dismissal for a second yellow card offence, the former Lazio midfielder rifled the ball home when Romero failed to deal with an early cross into the D.
Tempers began to flare at a heated Marassi with the midfield scrap precluding either side from mounting a promising raid as time ticked away.
Samp's Daniele Gastaldello headed just wide of his own goal under pressure from Borriello two minutes from full-time.