Rovers had not lost at home in 11 games since Sean O'Driscoll took charge in September and had not conceded a goal in their last seven home matches.
Last season they knocked Manchester City and Aston Villa of the Carling Cup and this was seen as a tricky test for the Premier League side.
But Sam Allardyce's men showed their mettle to win in convincing style despite making seven changes to their starting line-up.
Nicolas Anelka and Gary Speed were among those rested to the bench, but Bolton could still boast eight internationals in their starting eleven and it proved more than enough.
The writing was on the wall for Doncaster as early as the eighth minute when Kevin Davies slotted home an angled shot after Stelios Giannakopoulos had set up the chance.
Stelios set the standard for Bolton with a performance full of skill, pace and power closely matched by Davies and impressive Iranian star Andranik Teimourian.
Rovers survived appeals for a penalty when Stelios appeared to be brought down by James O'Connor in the tenth minute.
Doncaster had not got to grips with the opposition or the pace of the game at that stage.
But they gave Bolton a fright when a tremendous header from Mark McCammon was tipped away by Ian Walker at full stretch following a 12th minute free-kick.
Adam Lockwood sent a glancing header just over the top a minute later, before home keeper Ben Smith produced a super save to keep out a cracking effort from Teimourian.
Teimourian was not to be denied however and after Smith did well to parry another shot in the 22nd minute, he followed up to slam home the second goal.
The tie was as good as over when Bolton made it 3-0 in the 33rd minute, with Israeli international Idan Tal racing through to fire past Smith.
Teimourian added a fourth early in the second half for good measure when he blasted home in fine style after skipping past a challenge from O'Connor.
Bolton's attitude and work rate never flagged even when they were four in front and they were determined not to concede a goal as they pulled players back to protect their lead whenever Rovers tried to attack.
Paul Heffernan missed a couple of chances for Doncaster when he failed to connect with the ball with the goal at his mercy, but overall Bolton finished more than worthy winners.