The 19-year-old striker latched onto a long throughball from Emmanuel Petit, brushed aside Gudni Bergsson before sliding past Jussi Jaaskelainen and slotting home from three yards on 52 minutes.
"The little lion is growing up very well," smiled Chelsea boss Claudio Ranieri.
That was the young striker's seventh goal for Chelsea in just 15 outings - his third start in the Premiership.
"He is a very dangerous player," added Ranieri. "He is the focus for the team. Everything he did was dangerous to Bolton.
"But I am happy with the victory. We created many chances and when we did not score I was a bit worried in case they got a lucky break and won the match."
Chelsea remain clear in fourth place but significantly they are just a point behind Newcastle United.
"I'm not looking at teams above us," claimed Ranieri. "I am looking behind me at Everton and Liverpool.
For Bolton's part this was a game they wanted to get out of the way without injuries before next week's six-pointer against West Ham United at the Reebok Stadium.
Bolton boss Sam Allardyce admitted as much saying: "I felt we could have got a point, especially when we started to play well in the second half.
"Their goal came against the run of play. Overall, perhaps, they just deserved it."
Bolton remain three points ahead of third from bottom West Ham: "If we beat them then we will be virtually safe," Allardyce added.
"It won't be certain, but we will be doing everything possible to win."
This match was a dour affair with Bolton failing to have a single shot on target.
Apart from Cole's goal, he had an earlier golden chance when on 32 minutes Boudewijn Zenden clipped an angled ball into the penalty area. Cole, arriving late, chipped the ball over Jaaskelainen's body but it also went just over the crossbar.
Jimmy Floyd Hasselbaink had two glorious chances to rebuild his shattered confidence - both times he fell foul to excellent anticipation saves by Bolton's man-of-the-match Jaaskelainen.