Goals from Inigo Idiakez, Tommy Smith and Paul Peschisolido helped Derby seal a play-off place and leap-frog above North End into fourth spot.
Idiakez gave the Rams the lead with a quick free-kick and Smith made it 2-0 after good work from Jeff Kenna.
Patrick Agyemang's close range finish gave Preston hope with 21 minutes left.
But Peschisolido's last-gasp goal sealed Derby's win, and the clubs will meet again at Deepdale next week in the first leg of their play-off semi-final.
Derby had needed a point to be sure of a place in the top six but ended up taking all three.
They did so without leading scorer Grzegorz Rasiak who had undergone groin surgery, and Rams boss George Burley made four changes from the side thumped 6-2 by Coventry last week.
Tom Huddlestone, Richard Jackson, Marco Reich and Peschisolido came in for Mo Konjic, Chris Makin, Ian Taylor and Marcus Tudgay.
A swirling wind meant neither side could settle in the early stages but there were still chances at both ends.
Morten Bisgaard fired over the crossbar for Derby before Preston captain Graham Alexander's shot was comfortably saved by home goalkeeper Lee Camp.
Smith hit the post for Derby just before the interval and there was still time for Idiakez to give the Rams the lead before the half-time whistle was blown.
In stoppage time, Smith was brought down by Dickson Etuhu 25 yards from goal and from the free-kick, Idiakez cleverly struck early to send a right-footed shot low to the left of a stationary Carlo Nash.
The Rams extended their lead in the early stages of the second half after a surging run down the right flank by Kenna.
He found Peschisolido who set up Smith at the far post to finish a flowing move.
Preston did not lie down and kept coming forward themselves.
They pulled one goal back on 69 minutes when Agyemang was on hand to bundle the ball over the line after Camp had clawed away a Claude Davis header.
But their hopes of a comeback were virtually ended with 10 minutes left when Alexander had to limp off injured with all three substitutes used.
Peschisolido was then spectacularly denied by a superb Nash save before sealing Derby's win in the final minute.
He latched on to a long ball by Richard Jackson and nutmegged the keeper to make it 3-1.
The Rams will now have home advantage in the second-leg of their play-off semi-final.
Derby manager George Burley:
"These players have surprised me, they've proved me wrong.
"I said at the start of the season we couldn't finish in the play-offs but the players have showed great consistency, great quality, plenty of discipline and also played the game in a great style.
"It's no secret we haven't got the biggest squad in the world but look at Leicester, who are basically a Premiership set-up, and look how far down the table they've finished this season.
Preston manager Billy Davies:
"I'm disappointed by the result but we went to Derby with a gameplan and that was to make sure everyone was prepared for the next two play-off games.
"We rested one or two people and also gave games to people who needed it - like big Patrick Agyemang up front - so we chopped and changed a little bit.
"But the most important thing was that we came through in good shape for the next two games."
Derby: Camp, Kenna, Johnson, Jackson, Huddlestone, Bisgaard, Smith (Holmes 72), Bolder, Idiakez (Taylor 72), Peschisolido, Reich (Konjic 90).
Subs Not Used: Miller, Junior.
Goals: Idiakez 45, Smith 49, Peschisolido 90.
Preston: Nash, Alexander, Mawene (Broomes 45), Davis, Hill, Mears, Etuhu, McKenna, Sedgwick (O'Neil 52), Agyemang, Cresswell (Nugent 66).
Subs Not Used: Ward, Lucketti.
Booked: Mears, O'Neil, Hill.
Goals: Agyemang 69.
Ref: P Crossley (Kent).