The Spanish defender equalised with a drilled strike for Rafael Benitez's third-placed side with three minutes left.
"It's a missed opportunity," said Napoli's Switzerland midfielder Gokhan Inler. "We tried to play a bit faster in the second half. We had a bit of bad luck as we hit the post and (had) a few chances, but we couldn't do it.
"We looked to win the game but it wasn't easy because they kept it tight and broke well. We need to work on closing these games out."
The draw was harsh on a well-organised Chievo side, who stay 16th on 18 points, a point above the drop zone, despite their Napoli fan Gennaro Sardo scoring with a rising, angled shot in the 18th minute after a slick one-two with Cyril Thereau.
The draw comes after a lacklustre attacking display from the hosts, who were nevertheless unlucky in front of goal.
Striker Gonzalo Higuain missed an open goal in the first half, Dries Mertens twice hit the post and substitute Lorenzo Insigne struck the bar with a powerful shot.
It was another disappointing home result for Napoli after a defeat by Parma and draws against Sassuolo and Udinese in the first half of the season.
Napoli trail AS Roma by three points before they visit Hellas Verona on Sunday (1130 GMT) and are four points ahead of fourth-placed Fiorentina who host Genoa in Sunday's late game (1945 GMT).
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- Rafael Benitez