The Royals missed out on the play-offs despite a spectacular equaliser by Gareth McCleary at home to Burnley.
Reading are back in the play-off places following a 2-0 victory over Middlesborough in the Championship.
Nigel Adkins' new side Reading FC played host to his former team Southampton FC at the Madejski Stadium. The Saints beat the Royals 2 - 0.
he Birmingham goalkeeper was beaten again in the 75th minute. Dan Burn fouled Robson-Kanu on the edge of the area and Guthrie curled home a fine free-kick via Randolph's near post to complete** **Reading's comfortable win.
Full coverage of all today's fixtures on the ITV Sport website here
Birmingham failed to capitalise on their early superiority and Reading responded with a series of swift breaks. Garath McCleary released Pavel Pogrebnyak inside the Birmingham area but the Russian's fierce shot was well saved by Darren Randolph.
Reading's pressure finally paid off in the 32nd minute as they took the lead, albeit with a goal that was tinged with good fortune.
Chris Burke was penalised for handball and Guthrie's free-kick from wide on the left did not appear to carry too much danger. Yet it somehow found its way through a mass of bodies in the area and nestled in the far corner of Randolph's net.
Both of Guthrie's goals come from free-kicks - the first unintended, as it flew through a packed Birmingham penalty area, and the second an accurate set-piece that found the net via a post.
Those goals helped Reading make it 13 points from their last five league games and leave Birmingham unable to cap a memorable week with a third successive victory.
Lee Clark's men beat Sheffield Wednesday 4-1 in the league last time out and then followed that up with a 3-1 cup win over Swansea, and buoyed by those successes they started brightly.
Reading had won nine of their previous 11 games against Derby but came into the match with seven first-teamers missing, which meant a first league start for 19-year-old Jordan Obita.
The Royals had not conceded in 285 minutes of Championship football but their defence was almost breached in the eighth minute when Johnny Russell got in on the left and Alex McCarthy could only push out his low shot but Craig Bryson could not turn in the rebound.
The Russian striker found the net for the first time since January and although Will Hughes gave Derby hope, sub Nick Blackman secured Reading's 10th win in 12 games against Derby who have yet to record a home Sky Bet Championship victory this season.
Reading keeper Alex McCarthy kept the visitors in the game in the first half but Pogrebnyak pounced in the 47th minute after a free-kick was knocked down and the side-footed his second in the 62nd minute when Derby failed to clear a cross.
Hughes beat McCarthy with a curling shot in the 80th minute which was the first goal Reading had conceded in 365 minutes of Championship football but Blackman wrapped up the points in the fifth minute of stoppage time.
Yeovil again dictated proceedings at the start of the second half, with on-loan striker Andy Williams coming inches away from breaking the deadlock after hitting a curling effort narrowly wide.
However, Huish Park once again became the centre of controversy on 77 minutes after referee Trevor Kettle awarded the Royals a penalty after Luke Ayling was adjudged to have brought down Le Fondre.
The striker picked himself up and slammed past goalkeeper Wayne Hennessey to net his third league goal of the season and earn the visitors the valuable three points
In the first ever league meeting between the sides, Adam Le Fondre's penalty 13 minutes from time handed the Royals their first Sky Bet Championship win since the opening day - and condemned the Glovers to a fifth consecutive defeat in all competitions.
Reading manager Nigel Adkins made sweeping changes after the Royals' 6-0 humiliation at Peterborough United - with only Chris Gunter, Shaun Cummings and Le Fondre surviving the cull.
Adkins swapped Gareth McCleary for Danny Williams in a surprise first-half substitution and the newly-introduced midfielder came closest for the Royals before the break when he volleyed former Real Madrid and Everton winger Royston Drenthe's deep cross wide of the post.
The home side enjoyed the better of the first half, with Ricardo Fuller dangerous in attack, but the Royals went closest to breaking the deadlock through Royston Drenthe's free-kick, which was saved by Matt Gilks, and Jem Karacan's 18-yard effort that came back off the crossbar.
Gilks then saved at the feet of Adam Le Fondre in the second period but substitute Barkhuizen stole the show with a run and finish on 75 minutes to seal the points for the hosts.
Reading's central midfield pairing of Karacan and Danny Guthrie were struggling against the Tangerines' dominant midfield trio and Paul Ince's side fashioned their best opportunity of the half midway through the opening period.
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That seemed to spark Watford into life and they got themselves back into the game in the 66th minute when Faraoni headed home an Almen Abdi cross from close range. It looked as though the game was over minutes later when Karacan restored the two-goal advantage with a neat finish on 70 minutes.
But Watford were not done as once again they got themselves back into the game - this time from the penalty spot.
Guthrie pulled Fabbrini down in the area and referee Mike Jones had no hesitation in pointing to the spot.
Deeney stepped up to coolly slot the ball past McCarthy and, with stoppage time fast approaching, Fabbrini prodded the ball past McCarthy from close range to rescue a point.