Chievo had frustrated Inter throughout, but just when it looked like they had done enough to earn a point, Walter Samuel headed Inter in front.
Diego Milito, who missed a penalty in the 14th minute, sealed the win in stoppage time to lift some of the pressure from Inter coach Claudio Ranieri and give the Nerazzurri a boost ahead of the second leg of their Champions League last-16 tie with Marseille next week.
Inter were gifted the chance to take the lead in the 14th minute when a corner from the right crossed the penalty area and hit the arm of Francesco Acerbi as he tried to clear the danger.
The penalty was inevitable, but Milito failed to take full advantage as Stefano Sorrentino made his third penalty save of the season to deny the Argentinian.
Wesley Sneijder started to take matters into his own hands and, ghosting around the penalty area on the shoulders of the two strikers Milito and Diego Forlan, he appeared to enjoy his licence to roam.
In the 18th minute, he found room on the edge of the area to curl in a shot off the top of the crossbar.
Chievo had little choice but to defend, although they did come close to scoring in the 42nd minute when Sergio Pellissier found a way around the back, but Lucio just did enough to unbalance him and his shot was saved by the legs of Julio Cesar.
Just before the referee sent the teams back to the dressing room for a break, Sneijder's shot was blocked by the hands of Paolo Sammarco, but this time the referee did not point to the spot, judging the Chievo player to be too close the shot to get his arms out of the way.
Sneijder created the first chance of the second half when he lifted the ball to the far post where Andrea Poli slid in but shot wide on the stretch.
The Dutchman's shot was parried in the 85th minute with Esteban Cambiasso sending the rebound over as it looked increasingly like the Nerazzurri were going to come away with only a point.
But their luck turned in the 87th minute when Samuel scored his fourth career goal against Chievo with a diving header past Sorrentino.
Milito then sealed the win in the last minute with a header from Javier Zanetti's cross to earn Inter a much-needed win.