It was Palace's third win in four games, all of them at Selhurst Park.
Doncaster, who are now without a win in four league matches, started well, James Hayter missing two good opportunities but Palace took the lead through Counago's second of the season 10 minutes before the break.
There were chances at both ends in the second half with Wilfried Zaha hitting the post for Palace but home goalkeeper Julian Speroni also saved well from Brian Stock and John Oster.
Doncaster had the better of the opening stages with two chances falling to Hayter within the first 15 minutes. He first headed over from James Coppinger's chipped ball through before heading wide from Coppinger's near-post corner.
The home side created their first opportunity after 24 minutes, Darren Ambrose's cross was met by Neil Danns but his right-footed 12 yarder was well saved lowdown by Doncaster's veteran goalkeeper Neil Sullivan.
Doncaster remained dangerous and created two opportunities just after the half-hour. But Hayter, who was one-on-one with Palace goalkeeper Speroni, was well tackled by Anthony Gardner before Speroni tipped over David Healy's overhead kick.
Palace then took the lead after 35 minutes.
Ambrose enjoyed a run down the right and passed to Counago on the right side of the area, the striker finishing well slotting a right-footed shot
between Sullivan and his near post.
Rovers started the second half as they began the first Coppinger having a good chance to equalise after 52 minutes but his effort was straight at Speroni from 15 yards.
The home side then had a great chance to double their lead a minute later. Counago threaded a ball to James Vaughan who was one-on-one with Sullivan but he could only hit his shot straight at the keeper.
Counago himself then had a shot from the edge of the area which Sullivan did brilliantly to tip round the post before Zaha dribbled his way into the box and unleashing a shot which hit the post.
Doncaster went up the other end and Speroni did excellently. First tipping over Healy's effort before doing even better to fingertip wide Brian Stock's 25-yard volley two minutes later.
Sean O'Driscoll's side kept pressing for the equaliser and Oster forced Speroni into a great save with a shot from the edge of the area before Healy had their last chance three minutes from time but Speroni again was up to the challenge.