Derby remain rooted to the bottom of the table and 10 points away from safety after Stelios Giannakopoulos scored the only goal of the game in stoppage time for Bolton at the Reebok Stadium.
The Greece international fastened on to a long ball from the back, lifted the ball past Lewis Price and nodded home.
Derby still had a chance to level - Jussi Jaaskelainen saving Kenny Miller's shot with seconds to spare.
The dramatic late finish was harsh on Derby who deserved something from the game - but their survival hopes now lie in tatters.
The Rams are still 10 points adrift of safety with just 17 games left and must surely now start planning for an immediate return to the Championship.
Bolton manager Gary Megson said: "We didn't pass it, we didn't support the ball, I cannot say that we fully justified the victory.
"It's a great reward for us playing as badly as we did. We didn't do enough to suggest we could win but we kept going.
"If I was the Derby manager, I'd be saying that was a bit unjust. But we're told they even themselves out."