City player-manager Gary McAllister set up the first for substitute Jay Bothroyd in the first minute after the restart and then youngster David Pipe celebrated his first league start by scoring his first senior goal for the club.
McAllister celebrated with a double-fisted salute to the travelling Sky Blues fans at the end after they dominated the game in the second half leaving Gills boss Andy Hessenthaler to reflect on his team's most disappointing performance of the season so far.
He said: "We don't become a bad side over one performance. I just felt we were not in the game but it wasn't for a lack of effort because my players always give 100 per cent.
"However, you've got to give Coventry some credit as well because they came and made it very hard for us.
"They put pressure on us all the time and made it very difficult."
Rod Wallace made his long overdue home debut but suffered from a lack of service and was eventually taken off just before the hour mark.
Coventry lost midweek hat-trick man Gary McSheffrey with a facial injury and concussion after only 17 minutes.
Scorer Bothroyd was also booked and then substituted himself with just over a quarter of an hour left by Moroccan international Youssef Chippo and he was also booked for kicking the ball away at a free kick.
Coventry defender Mo Konjic played with a facial cast protecting a broken cheekbone. He was also booked for a heavy challenge on Leon Johnson, also making his home debut but taken off with Wallace.