Gary Johnson’s side were dominant in the opening stages and forged ahead in the 13th minute.
Striker Nicky Maynard was pushed in the back by Jay Tabb and referee Mark Haywood instantly pointed to the spot.
Reading were furious with the decision, with substitute Church booked on the sidelines for his protests, but Hartley was undeterred and smashed the spot-kick high into the net.
Shane Long then headed over from close range as he stretched to meet Jobi McAnuff’s cross before Church entered the fray.
And he made an immediate impact in the 90th minute when he converted Jimmy Kebe’s low cross at the near post before celebrating with fans and being shown a second yellow card by Haywood.