McIndoe kept his cool to tuck away the kick and pull Rovers level on points with the Latics in the bottom half of League One.
Both clubs have had a disappointing season so far and it showed in a match of poor quality which featured few real chances to break the deadlock.
Doncaster had the best of them and Oldham, who were riding high in the table in September, have won just one game out of their last six.
The away side dominated the first 20 minutes but could not get past an Oldham defence which had conceded seven goals in its last two league matches.
At the other end Doncaster's back-line also stood firm and only allowed one chance in the first half which saw Paul Warne have his shot deflected for a corner.
Oldham could have taken the lead on 47 minutes when Chris Porter's run down the right ended with a cross to strike partner Andy Liddell.
Liddell connected well with a drive from ten yards but keeper Jan Budtz saved with his left boot.
Doncaster then took control and Paul Heffernan had a lob cleared off the line by Latics left-back Marc Tierney.
Midfielder Ricky Ravenhill shaved the woodwork from 20 yards and substitute Simon Marples brought a save from Chris Day at his near post.
Day made a flying stop from McIndoe after 72 minutes but there was no stopping Doncaster six minutes later when they launched a quick counter-attack.
Lewis Guy's dash into the box was halted by a clumsy challenge from Terrell Forbes and McIndoe sent his penalty to the keeper's right to seal it for Rovers.