Unfortunately for Savage - a player never too far away from controversy - he was not at the races as the Royals secured fifth place and a two-legged clash with Cardiff.
Ian Harte, enjoying an Indian summer at the Madejski Stadium, scored his 13th goal of the season from the spot to open the scoring, but Jamie Ward equalised from Derby's first real chance.
Daniel Ayala, who had brought down Simon Church for Reading's opener, then fouled Michail Antonio in the area for a second penalty, but this time Harte hit the post from 12 yards.
They were not to be denied, though, and a scruffy strike from Hal Robson-Kanu after 72 minutes secured a deserved victory.
Reading made six changes as boss Brian McDermott had one eye on the club's play-off campaign.
Church and Mathieu Manset started in attack, while Robson-Kanu, Jay Tabb, Shaun Cummings and Alex Pearce also came in.
Derby handed full debuts to young goalkeeper Ross Atkins and striker Callum Ball. Dean Leacock started for the first time since the end of January, Ward was back after a ban, while Savage was playing the final game of his career.
The Royals started brightly, with Manset fizzing a shot wide from distance in the third minute.
The January signing from Hereford was looking dangerous and he came close again shortly afterwards, racing clear and dinking the ball over Atkins, but his effort also cleared the crossbar.
Winger Robson-Kanu sent a diving header just wide, before Church cut inside and unleashed a superb shot from 22 yards which crashed back off the crossbar.
It was all Reading, and they took the lead from the penalty spot after 24 minutes.
Savage gave the ball away to Church and he was brought down by Rams defender Ayala in the box. Veteran full-back Harte stepped up to confidently despatch his spot-kick.
Derby had offered little but found themselves on level terms in the 32nd minute. Ward collected the ball 25 yards out and sent a stunning swerving effort past Adam Federici and into the bottom corner.
Ball volleyed wide from just outside the box, before the Rams had the ball in the net again, only this time Stephen Pearson was flagged for offside.
Reading spurned the chance to go into the interval in front as Harte thumped the base of the post with his second spot-kick after Antonio had brought another foul from Ayala in the area.
April's manager of the month McDermott saw his men take control of the second half, with Church and the lively Robson-Kanu both seeing shots deflected wide.
Derby's response came from substitute Ben Davies, but Federici got down well to push away his low drive in the 65th minute.
Man-of-the-match Robson-Kanu grabbed the winning goal in the 72nd minute.
Brynjar Gunnarsson won the ball which looped up for Church and his header found its way to Robson-Kanu who squeezed the ball in via a deflection.
Church could have sealed the win but his right-foot curler was saved by Atkins, while at the other end Federici proved the hero with a superb stop to keep out Jeff Hendrick's thunderbolt.