An own-goal from Matt Mills and an Andrew Surman penalty gave Southampton their second Championship win of the season at the Keepmoat Stadium.
Doncaster's Darren Byfield was denied on 23 minutes when Saints keeper Kelvin Davis tipped his header past the post.
Mills then turned the ball past his own keeper Neil Sullivan after 50 minutes.
Surman netted eight minutes later when Richie Wellens fouled Adam Lallana, and the midfielder won a second penalty on 79 minutes only for Sullivan to save.
Doncaster boss Sean O'Driscoll: "We started really brightly and in the first half looked like we were going to score.
"In the second half we held them off for five minutes and perhaps we were a bit gung-ho and if you throw caution to the wind teams are set up to counter-attack and defend.
"Perhaps we lost our discipline after the first goal and ended up being 2-0 down and that's something we need to learn from."
Southampton manager Jan Poortvliet: "We had a difficult time in the first half and this is a young team and when some things happen they need to calm down.
"Today they did that and they showed great spirit in the second half and I think we worked hard until the end, helping each other.
"At half-time I told the players to break quickly because when we do that we look like we are going to score.
"So I am very happy with the result and it will give us a lot of confidence into the next few games."
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