The substitute netted from close range after Nigel Pearson's men had failed to clear Ian Harte's free-kick.
It was just reward for the Royals, who had seen a Shane Long penalty saved by Vito Mannone after Paul McShane had cynically brought down the striker.
However, Hull will feel they should have claimed victory after hitting the woodwork twice through Robert Koren and Cameron Stewart.
James Harper, who spent nine years at the Madjeski Stadium, had put the Tigers in front in the first half when he drilled a long-range effort past the helpless Adam Federici.
That looked to be enough to seal the win, but Church ensured the spoils were shared as both sides extended their unbeaten streak to eight matches.
Both teams came into the match in buoyant mood after Boxing Day wins as Jimmy Bullard's last-gasp strike gave Hull a 3-2 win at Sheffield United, while Long netted twice in Reading's 4-1 win over Bristol City.
It was the hosts who started brightly and Federici had to be at his best to deny Kamil Zayatte and Koren.
Jamie Devitt's near-post corner was flicked on by Zayatte and Federici did well to tip the ball round the post, while Koren's strike from the edge of the area was sharply saved.
The Tigers' top scorer then beat Federici with his next strike from the edge of the box after shaking off the challenge of several Reading defenders, but this time he was denied by a post.
Reading felt they should have been awarded a penalty when Noel Hunt went down under a challenge from Zayatte, but referee David Foster was not interested.
Harper then put Hull in front with a wonderful goal in the 39th minute to leave the visitors feeling more aggrieved.
The former Royals midfielder collected the ball and unleashed a shot from 25 yards that sailed past Federici.
Stewart's deflected strike came back off a post as Hull looked to be in the ascendancy before half-time.
Confusion reigned at the beginning of the second half when Andy Griffin tackled Jay Simpson on the edge of the Reading area and although Foster looked uninterested, one of his assistants flagged for a penalty.
However, after almost five minutes of confusion, play resumed with a drop ball.
Reading were eventually awarded a penalty in the 64th minute when McShane made a rash challenge on Long, who saw his effort brilliantly saved by Mannone, who is on loan from Arsenal.
However, Mannone was at fault when Church scored a deserved equaliser in the 82nd minute.
Harte's inswinging free-kick should have been dealt with by Mannone, but he only palmed the ball into the path of Church, who netted from a yard out.