Eder's first-half header was enough to earn Samp all three points and extend their unbeaten run to five matches in all competitions.
The defeat brought an end to a four-match winning run for Eugenio Corini's Chievo, who remain just above the relegation zone.
The home side had the first chance after six minutes as Cyril Thereau played a good ball into the six-yard box for Alessio Sestu, who tried a chip over Angelo Da Costa but the Samp goalkeeper pulled off a great save.
The opener arrived for Sinisa Mihajlovic's side 10 minutes later as Eder met the ball in the box to head home from a corner for his sixth goal of the season.
The home side almost pulled one back as Sestu tried his luck from outside the box but his effort sailed high over the crossbar.
Then, on the brink of half-time, Lorenzo De Silvestri almost doubled Sampdoria's lead but he too fired too high over from just outside the box.
The Flying Donkeys came out strong after the break and Sestu had a chance to level with a powerful shot but the ball went over the bar.
And Manolo Gabbiadini was left to rue his missed chance to score the visitors' second as he fired over after getting past Christian Puggioni.
Chievo pressed for an equaliser in the closing 15 minutes and Da Costa had to work hard to keep them out.
Substitute Dejan Lazarevic was first to try his luck from inside the box but Da Costa saved in the corner.
Sergio Pellissier came close with a header while Sestu blazed over late on as Chievo ran out of ideas.