The two sides initially met on August 24, only for the match to be abandoned at half-time due to a waterlogged pitch with Rovers leading 3-1.
Doncaster boss Paul Dickov expressed dismay at the decision and is likely to be more frustrated after seeing his side suffer defeat this time around.
Stephens opened the scoring in sublime fashion, volleying into the top corner from 20 yards six minutes before half-time.
Charlton's lead was then doubled on the hour mark as Johnnie Jackson set up Simon Church for the Wales forward's fifth club goal of the season.
Doncaster could have few complaints with the result, having seen Yann Kermorgant and Cameron Stewart strike the woodwork for the hosts.
Victory lifts Charlton six points clear of the Championship relegation zone and ahead of Doncaster, who lie 20th.
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