Debutant Harte wanted to take the first spot-kick in Saturday's Championship clash but was denied by Long, who converted from 12 yards. Hart then did get his chance after the break and copied his fellow Irishman by smashing the ball home.
Jimmy Kebe added a third in stoppage time.
Reading sold Gylfi Sigurdsson to Bundesliga side Hoffenheim on transfer deadline day for a club record fee but Brian McDermott did hand a debut to former Leeds left-back Harte.
Palace midfielder Edgar Davids was absent for personal reasons but George Burley did have on-loan Everton forward James Vaughan in his side for the first time.
In a bright start, former Eagles winger Jobi McAnuff found space on the left before finding Long inside the area. He looped a ball to the far post where Kebe thrashed in a volley across the face of the goal but narrowly wide.
Palace captain Paddy McCarthy then had a decent sight of goal from a set-piece but shot wildly over the crossbar before McAnuff almost silenced the boo boys in the away end with a low shot which Julian Speroni gathered easily.
Royals captain Matt Mills then thought he had opened the scoring with a fine header from a Brian Howard corner but the ball struck the face of the crossbar.
Mills was unlucky but Reading did go ahead moments later in the 37th minute.
Long turned McCarthy far too easily and when he was tripped by the central defender, Republic of Ireland international Long kept his cool to score from the spot.
Sigurdsson was the regular penalty taker and Harte was keen to take the kick but Long made no mistake.
Jem Karacan then crashed a long-range shot just wide as the Royals ended the half on a high.
Burley brought on Ipswich loanee Pablo Counago at the break but it was Long who nearly found a second goal when he burst into the area and flashed a shot wide.
And Harte doubled the advantage in the 65th minute with another spot-kick.
Julian Bennett was the offender this time as he tripped the lively Long and this time Harte was allowed the chance to bury his effort and give the hosts all three points.
Kebe made it three in the final seconds when he ran on to Howard's pass and clinically finished from the edge of the area.