Chievo also gave new coach Eugenio Corini a winning start while promoted Sampdoria's campaign has stalled after a bright opening.
David Di Michele's long-range effort appeared to pose little threat to Romero but the keeper mistimed his jump and allowed the ball to slip through his hands and go in under the crossbar in the 87th minute.
Sampdoria's players protested angrily that Chievo should have kicked the ball out of play earlier in the move as midfielder Pedro Obiang was down with an injury.
Earlier, Cyril Thereau gave Chievo the lead in first-half injury time with a clinically-taken goal and a lacklustre Sampdoria levelled just after the hour when Enzo Maresca curled in a free kick.
Chievo's win lifted them to fifth from bottom with six points.
Sampdoria are in fifth place, with 10 points from seven games having had one point deducted before the season began for their involvement in a match-fixing scandal.
They won their first three matches, drew the next two and have now lost two in a row.
Corini, who has never coached a Serie A side before, replaced Domenico Di Carlo who was fired on Tuesday.