Billy Sharp had missed a penalty in the midweek 1-1 draw at Preston but made no mistake this time around as he opened the scoring in the first half before Emmanuel-Thomas added the second.
Rob Hulse reduced the deficit 16 minutes from time but Rovers held on to claim maximum points at the Keepmoat Stadium.
Elliott Ward, who was playing the final game of his initial loan spell with Rovers, spurned a half chance in the early stages as he failed to get in a decent strike following a scramble in the box.
Derby's David Martin, who was recently drafted in on a month-long loan from Liverpool, was given his debut after first-choice goalkeeper Stephen Bywater was forced off with a back injury in Wednesday's defeat at Reading before his replacement Saul Deeney was sent off.
Captain Robbie Savage played in goal for 50 minutes against the Royals, but it was Martin who took over in South Yorkshire.
But Martin was beaten after just 15 minutes as Sharp netted his 15th goal since arriving on loan in September after being pulled down by Jake Buxton in the box.
The visitors should have levelled midway through the first half but Hulse hit a post and Steven Davies, who started up front for the first time since January, could not get onto the end of the ball and Stephen Pearson shot tamely at Neil Sullivan in the Doncaster goal.
Derby soon wasted another chance to level as Michael Tonge's shot was well blocked by defender Gareth Roberts.
And those misses almost proved costly as Doncaster pressed for a second goal before half-time, but James Coppinger curled a right-footed shot wide before Sharp saw his strike comfortably saved by Martin.
Doncaster had to survive an early scare in the second half as Emmanuel-Thomas collided with Jay McEveley but fortunately for Rovers he was able to continue after receiving treatment off the field.
The midfielder netted his third goal for the club to increase the hosts' advantage in spectacular fashion.
Derby were given hope of a comeback when Hulse was given far too much space in the area to fire a left-footed shot beyond Sullivan, but it was not enough to prevent the Rams from crashing to their second defeat in four days.