The Flying Donkeys were denied an historic fourth straight win by Torino in the last game of 2012, but Ghana international Cofie ensured a fourth win from five outings with his powerful strike shortly before half-time.
Atalanta, meanwhile, slip below their hosts and into 12th place after suffering their fifth defeat from seven games, despite the best efforts of strikers Giuseppe De Luca and German Denis on the counter-attack.
The Nerazzurri displayed a verve rarely seen on their travels this season with a confident display throughout the early exchanges, with Cristian Raimondi soon forcing a fine save from Stefano Sorrentino from a few yards out.
De Luca stole the ball on the left flank to provide a fine cross into the centre, with no visiting player there to meet it, before repeating the move a few minutes later.
There was no team-mate on that occasion either and Chievo capitalised on the wasted opportunities to open the scoring against the run of play.
Cyril Thereau stole a march down the left wing in the 37th minute, picking out 21-year-old Cofie to slam the ball home on the volley.
De Luca's close-range effort provided cause for concern to the Chievo backline, though, with Bojan Jokic putting his body on the line to maintain the hosts' narrow lead going into the break.
Thereau danced past an opponent to find himself in front of Andrea Consigli as play resumed, but he could only find the side-netting.
Chievo upped the tempo and Roberto Guana was unlucky not to find the target in the 58th minute, his ripping effort spinning out for a corner.
De Luca and Ivan Radovanovic tried their luck from distance but Atalanta were being frozen further out of the game as time ticked away.
It fell to Denis to rescue a point on the end of a spectacular move, but despite the Argentinian's fine footwork in the final third, he was ruled offside.
Chievo soaked up the remaining pressure from the comfort of their own half and five minutes of stoppage time proved to be insufficient for Atalanta's cause.