The Liberty Stadium triumph on New Year's Day also handed Swans manager Brendan Rodgers a league double over his former employers.
Pratley netted in the 65th minute to inflict a first defeat in nine games on a visiting Royals side who enjoyed the majority of the chances and deserved a point but were repeatedly denied by keeper Dorus de Vries.
Simon Church also headed over from six yards late on when presented with a great opportunity to level matters, before Scott Sinclair came within inches of an injury-time second for the hosts, leaving Swansea celebrating their first double against the Berkshire side for 33 years.
City's lofty position in the league table will make pleasant new year viewing for Rodgers, who left the Madjeski Stadium in December 2009 after just over six months in charge in which he managed a mere five league wins.
The Northern Irishman made six changes for Tuesday's 1-0 triumph over Barnsley and he made a further four on Saturday as he continued to rotate his ranks over the hectic festive period.
Skipper Garry Monk came back in along with influential trio Sinclair, Pratley and Joe Allen.
Reading counterpart Brian McDermott also made four changes - striker Church and midfield trio Hal Robson-Kanu, Brian Howard and Jay Tabb all starting the New Year's Day fixture.
There was a pretty ordinary start to proceedings in south Wales but there was nothing routine about Dutchman De Vries 20 minutes in as he made two great stops, coming on the back of his heroics against the Tykes earlier this week.
First he threw a leg out to deflect Alex Pearce's stabbed shot wide before scrambling Howard's low drive behind from the resulting corner.
De Vries was then at it again just before the break, producing a stunning reaction save to turn wide Jimmy Kebe's flashing low cross-shot from out wide which had taken a strong touch off Shane Long.
The second half continued to be a tight affair and it was left for De Vries to once again come to his side's rescue in the 52nd minute with a well-timed block to deny Church on the six-yard line after he had been fed by Long.
Swansea were desperately in need of a change of personnel or tactics in a bid to inject some attacking spark with Reading's rearguard holding out.
But their breakthrough came in the 65th minute via a set-piece.
Mark Gower floated a well-rehearsed deep free-kick to Angel Rangel who chested the ball down before sending a half-volley goalwards which deflected into the path of Pratley and he fired the ball home.
Monk soon produced a superb double block to deny Kebe and Robson-Kanu as the visitors went in search of an equaliser.
The goal opened the game up but it was still Reading who were creating the better openings and Church should have levelled in the 83rd minute but headed over from Kebe's cross.
Nathan Dyer and Sinclair then both missed great chances to add a late second for Swansea, but in the end their wastefulness proved inconsequential.