Stephens hit a spectacular first-half volley and Church wrapped up the victory after the break as the Addicks won the rearranged Championship clash and climbed above their fellow strugglers into 17th.
Doncaster could not claim they deserved much better on the night - they did not force a single save out of Charlton keeper Ben Alnwick.
However, the fact Rovers were 3-1 up when this fixture was originally played in August, only for torrential rain to come to Charlton's rescue, will leave boss Paul Dickov feeling distinctly under the weather.
Instead, three months after they looked destined for defeat Charlton, who kicked off one place above the drop zone, registered only their second home win of the season.
They thoroughly merited their victory as well with Yann Kermorgant and Cameron Stewart also hitting the woodwork while Alnwick, only drafted in after regular number one Ben Hamer was injured in the warm-up, could not have wished for an easier debut.
The hosts should have gone ahead in the opening two minutes but Church missed a sitter, dragging his shot wide from six yards out after Jordan Cousins chipped the ball over the top.
Strike partner Kermorgant also came up with an uncharacteristic miss midway through the first half when he met a cross from Rhoys Wiggins 10 yards out only to scuff his shot against a post.
Moments later Church's low cross found captain Johnnie Jackson, who struck the ball well with his left foot but saw Rovers keeper Ross Turnbull pull off a stunning save.
Doncaster's only real chance fell to Federico Macheda, who led the Charlton defence a merry dance in the penalty area before blazing his shot over the crossbar.
And moments later, in the 39th minute, Charlton took the lead when Stewart's cross was headed clear to Stephens who crashed it back past the stunned Turnbull and into the top corner from 20 yards.
After the break Turnbull got down well to beat out Lawrie Wilson's shot, but he could do nothing to keep out Church's clincher on the hour.
The striker was sent clean through by a superb pass from Jackson and kept his cool to slide the ball past Turnbull and in off the foot of the post.
It could have been even worse for Doncaster, but Stewart's 25-yarder hit the crossbar and Church missed his kick in front of goal.
Nevertheless, Rovers still had to make the long trip home from The Valley empty-handed for the second time this season.