The Irish international converted from the spot after being fouled in the penalty area by Ian Pearce, who was sent off for the challenge.
It was a tough encounter with three players being substituted in the first half alone through injury.
Fulham looked better in the second half but could not find a way past the solid Reading back four.
The Royals goal came in the 17th minute when Doyle slotted home from 12 yards.
A sweeping move involving Glen Little and then James Harper caught Fulham on the back foot. Harper's pass was played perfectly into Doyle's path, but he was upended with a clumsy challenge from Pearce.
Referee Dermot Gallagher had no hesitation about showing the defender a straight red card and Pearce, to his credit, did little to contest the decision and headed straight for the tunnel.
Reading pressed forward looking to take advantage of their extra man, but the closest they came was when Seol tried his luck from distance, only to see his shot take a deflection off Steve Sidwell and sail wide.
That was Sidwell's last notable contribution as he was substituted soon after following an earlier injury. Reading boss Steve Coppell was then dealt another blow when Little also had to be brought off with an ankle injury.
Despite their numerical disadvantage, it was Fulham who had two good chances to level the scores in the dying minutes of the first half.
Brian McBride first planted his diving header straight at Marcus Hahnemann after Liam Rosenior had supplied the perfect cross.
Then, Collins John battled hard in the six-yard box before toe-poking the ball through Hahnemann's legs. His effort looked to be rolling over the line until Ivar Ingimarsson spared his goalkeeper's blushes with a fine goal-line clearance.
After the restart Claus Jensen had a great chance to put Fulham on level terms, but his effort from the edge of the box was well saved by the American goalkeeper.
As is so often the case, Fulham's ten men looked to have more creativity than Reading's full-strength side in the second period.
But for some careless passing they should really have put themselves on level terms after enjoying the majority of the possession.
They did have chances, and Zat Knight will be ruing his missed header in the 62nd minute that sailed over the bar from Jensen's corner.
Moments before that Tomasz Radzinski tried in vain to con referee Gallagher with a dive in the penalty area, but his appeals were waved away.
Reading had their chances too and John Oster should have put the result beyond doubt with 15 minutes to go. Stephen Hunt's pass found him in space, but the former Everton man fired over the bar.
Another ex-Everton player was causing problems at the other end in the form of McBride. The American fired wide from 25 yards but his shot was close enough to give Hahnemann a scare.
Reading had more chances at the death and Doyle was unlucky not to have added to his first half goal when he raced clear of the Fulham defence. But his shot was straight at Antti Niemi, who saved with his legs.
It was a gritty performance from Reading, while Fulham need to go back to the drawing board before they slip down the Premiership.