The Royals parted company with Brendan Rodgers earlier this week after a poor start to the season and chief scout Brian McDermott - in caretaker charge - took a much-needed point after a strong performance.
The Robins started well and came close in the second minute when Cole Skuse sent in a shot from the edge of the area which was turned over by Adam Federici.
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.
McDermott's side were sparked forward by the goal and came close to an immediate response.
Jobi McAnuff played in Grzegorz Rasiak on the break but the Poland international took a poor touch which allowed City goalkeeper Dean Gerken to make a sprawling save.
Maynard then sent a powerful shot just wide from the edge of the area before the Royals came close to a leveller.
Marek Matejovsky unlocked the City defence with a precise pass to free Gylfi Sigurdsson, who rounded Gerken with a smart touch.
Sigurdsson was forced wide but got a shot away, only to see Jamie McAllister slide in to hammer the ball clear.
Sigurdsson then forced Gerken into a save moments later from the edge of the area as Reading ended the half well on top.
Tabb was replaced at the break with McDermott bringing on the experienced figure of Brynjar Gunnarsson and Shane Long had the first sight of goal in the second period.
Again, Matejovsky was the architect when his pass over the top played Long through on goal but Gerken again came out quickly to shut down the angle and make a smart save.
Long then headed over from close range as he stretched to meet McAnuff's cross before Church entered the fray.
And he made an immediate impact in the 90th minute when he converted fellow sub Jimmy Kebe's low cross at the near post before celebrating with fans and being shown a second yellow card by Haywood.