The Dragons, who are now also above Scotland in the table, have a two-point advantage over Macedonia going into the final fixture of the campaign as they try to avoid the wooden spoon.
Despite missing several key players, including captain Ashley Williams and £86m-man Gareth Bale, the hosts had the better of a first half in which Hal Robson-Kanu felt he should have been awarded a penalty.
The referee was unmoved when the Reading winger seemed to be tripped as he advanced into the box on 30 minutes, and other Wales ventures forward in the opening period were also fruitless.
Neil Taylor was the first to test Macedonia goalkeeper Tome Pacovski, when he struck left-footed from outside of the box, while Craig Bellamy also called Pacovsk into action with a powerful drive, moments after Church headed wide at the near post.
Macedonia, though, were a threat on the break and had the best chance to break the deadlock before the interval when Nikolce Noveski rounded Wayne Hennessey, only to smash wildly over the crossbar.
When the action resumed, David Vaughan clipped the woodwork with a misdirected cross, and Wales's pressure was finally rewarded when Church applied the finish to a swift Dragons move.
Stand-in skipper Aaron Ramsey turned his marker inside the Macedonian half before releasing Bellamy, making his last home international appearance, down the right to cross for Church to fire confidently into the away net.
Ramsey had the chance to seal the points for his country when he was tripped in the box, but the Arsenal midfielder struck his penalty straight down the middle, allowing Pacovski to make the save.
Goran Pandev and Predrag Randjelovic went close to snatching an equaliser for the visitors in the latter stages, but Wales hung on to claim their third win of the campaign, and a much-needed one for Coleman.