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The 19-year-old striker lashed home an unstoppable 20-yard left-foot shot in the 69th minute to take his tally to three goals in three starts.
It appeared to be enough to finish off Derby after Billy Sharp had given Rovers the lead with a 15th-minute penalty.
But a moment of slackness at the back led to Rob Hulse pulling one back 16 minutes from time and Doncaster had to endure some anxious moments before the points were safely in the bag.
Derby looked a poor side throughout and seldom threatened in the first half apart from a 24th-minute effort which hit the foot of the post from former Doncaster midfielder Paul Green. By then Rovers were already in front.
Sharp had failed to convert a penalty in Rovers' last match but, when he was hauled back by Jake Buxton in the 15th minute, he had no hesitation in snatching the ball after the referee had pointed to the penalty spot and despatched the spot-kick with venom.
Green's effort failed to inspire the visitors and Derby were fortunate not to concede another penalty in the 34th minute when James Coppinger was brought down by Jay McEveley.
Doncaster were on top at the start of the second half with John Oster and Sharp going close before Emmanuel-Thomas hit his thunderbolt out of the blue when there appeared to be no danger.
Hulse's consolation effort failed to lift County and Doncaster put up the shutters in the closing stages, bringing on defender Shelton Martis for the creative Oster as they held out despite some uncomfortable moments in the closing stages.