Andrea Poli gave the home side the lead in the 33rd minute before the sleet turned to snow, and Eder struck the second with seven minutes remaining.
Chievo's attempts to find an equaliser throughout the second half were thwarted as they were left just eight points above the danger zone.
Just 30 seconds were on the clock when Gianluca Sansone burst through, but his effort was deflected behind for a corner.
Half an hour passed before the next chance arrived, and it was one which Poli took to put Samp in front.
He received the ball on the edge of the penalty area, shifted it to his right and then curled a shot unstoppably into the far corner.
Chievo's response was immediate with Roberto Guana's curling effort tipped behind expertly by Sergio Romero before Francesco Acerbi made an important intervention to turn Sansone's cross behind for a corner with Mauro Icardi lurking over his shoulder.
Icardi's route to goal in the 55th minute was blocked by Christian Puggioni, who had scampered 40 yards off his line to foul the Sampdoria forward.
Chievo then took charge of the game, forcing Samp onto the back foot, but failing to create any clear-cut opportunities.
Perparim Hetemaj went close with a volley as the visitors continued to press.
They then suffered the sucker punch after Cyril Thereau's shot was blocked in the 83rd minute and the ball was launched long for Eder, who held off two defenders before sliding the ball past Puggioni to seal the points for Samp with a classic counter-attack.