Two early goals put the Royals in the driving seat at Madejski Stadium - Garath McCleary and Roy Beerens scoring past Frank Fielding within the space of six first half minutes to secure a fifth successive win in the league.
The deadlock was broken when Samuel was tripped by Magnusson inside the Bristol box, McCleary's penalty was saved but he wrapped a right foot around the rebound to ripple the net. The second came when Gunter's superb cross was brilliantly volleyed home by Beerens and the hosts had control.
City threatened throughout though and Al Habsi had to pull out saves to deny Paterson, Abraham and Reid, before Gary O'Neil rifled home from the edge of the box with four minutes left. But four nervy minutes of stoppage time elapsed and Reading had three more points.
Manager Jaap Stam named an unchanged side, keeping with the eleven that earned a comfortable 3-0 home win over Burton the previous weekend. The only change to the squad saw Jake Copper come into the group as a substitute, replacing Danzell Gravenberch who picked up a knock in our midweek U23s cup game against Athletic Bilbao.
The first half chance fell our way, McCleary fizzing in a low cross towards Samuel 10 yards out and the striker getting a foot to it first only for the accompanying defender to deflect it wide with a timely block.
The same combination almost came good once more with the game eight minutes old. Moore swept the ball out wide to McCleary who beat his man to skid a low ball into the box. Samuel was looking for a decisive touch once more but this time Frank Fielding smothered it at the near post.
And Samuel was causing a nuisance. Minutes later a run in behind the Bristol City defence saw the young striker clipped by a Hordur Magnusson cutting across him - and referee Tim Robinson pointed to the spot. Garath McCleary stepped up to take the spotkick, Fielding saved low to his right, but McCleary pounced on the rebound to direct it into the opposite corner and hand the Royals an early lead.
The Robins responded with a sustained spell of pressure. Aden Flint wound up his right boot and lashed through a crowd of bodies inches wide of the bottom left corner.
However, Reading had a second on 19 minutes. McCleary dinked the ball over the top for Gunter who had scuttled into the City box. He volleyed a first time cross into the area and it dropped for Beerens who hit a spectacular first time volley of his own past a helpless Fielding and into the back of the visitors' net.
Lee Johnson's men carried a threat. Bobby Reid forced a tidy save from Al Habsi soon after the restart and then Lee Tomlin raced onto a corner that was pulled back into space but arrowed over the crossbar.
And Reid thought he'd pulled one back midway through the half when Jamie Paterson's low drive from a narrow angle was somehow kept out by Al Habsi's save against the body of Reid - the ball looping over the crossbar off the City man.
Our Omani pushed a Paterson cross to safety and Abraham was caught by the offside flag as he flicked it home after the whistle had blown. But Fielding had to pluck an Obita header out of the air before half-time.
Al Habsi had to shovel a Reid shot away from goal, McShane hoofing the loose ball clear before a City man could pounce the rebound. And Reading had a two-goal cushion at the interval.
Half-time: Reading 2-0 Bristol City
City signalled their second half intent with the first touch of the ball. Lee Johnson's men kicked off and Tammy Abraham powered forward through the Royals midfield before pulling the trigger just outside the box but aiming high over the crossbar at the end of a run full of purpose.
And Abraham got away from Moore to burst into the box soon after, pulling the ball back to tee up O'Neil for a shot that Al Habsi gathered in safely on his goalline.
Spurred on by more than 3,500 City fans, the visitors pressed again, this time Paterson dragging an effort wide of the bottom right corner from the edge of the Royals box.
Saves at both ends within moments of each other preserved the scoreline - Al Habsi pushing a Reid effort around the post after Fielding had parried a fierce McCleary drive. The game was open and looked to have more goals in it.
McCleary fed the ball into Samuel on the hour, just after City had made a double substitution, but the Royals striker couldn't find the target with his shot on the turn.
The game stayed open but some resolute defending from McShane, Moore and Blackett in the middle was doing enough to hold City at arm's length, substitute Aaron Wilbraham taking aim on the pivot but a sliding block from McShane and a clearance from Moore enough to thwart City.
With 12 minutes remaining, Abraham marauded forward again and after he was crowded out of a shot, the ball squirmed free into the path of Reid. He drilled a first time effort at goal but a superb diving block from McShane diverted the ball away from danger.
With five minutes left, Reading could have had a third. Obita's dangerous cross palmed to safety by Fielding before Williams's sidefooted effort from Harriott's cut back was blocked as it scuttled towards goal.
And City took advantage of those missed opportunities to pull one back soon after. Reading had scrapped the ball clear of their area, but only as far as Gary O'Neil on the edge of the box who whistled an effort inside the left upright to set up a tense finale.
Four minutes of injury time were survived, Abraham lashing over via a deflection to earn late, late corner. Fielding came up for it but as Ali Al Habsi claimed the ball in a crowded box, cheers rang around Madejski Stadium as it meant victory was ours. Five in a row.
Full-time: Reading 2-1 Bristol City
Reading: Al-Habsi, Gunter, Blackett, L Moore, McShane (c), Obita, Evans, Williams, Beerens (Kelly 90), McCleary (Harriott 74), Samuel (Meite 69).
Subs: S Moore, Watson, Cooper, Mendes.
Yellow: Moore, Beerens.
Goals: McCleary (13), Beerens (19)
Bristol City: Fielding, Little (Wilbraham 58), Flint, Magnusson, Bryan, O'Neil, Reid, Pack, Tomlin (Engvall 76), Paterson (O'Dowda 58), Abraham.
Subs: Lucic, Moore, Smith, Freeman.
Yellow: Bryan, Wilbraham
Goals: O'Neil (86)
Att: 18,778 (3,529 away)