The Lions kicked off knowing they needed a victory to ensure they beat the drop, otherwise they would be relying on results elsewhere.
And Martyn Woolford's first-half header settled the early nerves at The Den and proved enough to keep them in the second tier for a fifth straight season.
Victory provided Holloway with a successful end to an eventful campaign, which began with him struggling to adapt to the Premier League with Crystal Palace and ended with him keeping their south London rivals out of League One.
Things looked bleak for the Lions when he replaced Steve Lomas in December, and did not improve for the first couple of months, but a run of eight matches unbeaten when it mattered most has kept their heads above water.
The Bournemouth goal led a charmed life in the opening stages and visiting keeper Lee Camp saved well from Woolford at his near post.
A frantic goalmouth scramble then saw Stefan Maierhofer's header and Owen Garvan's follow-up blocked on the line before Steve Morison hooked the rebound over the top.
Morison came even closer to opening the scoring moments later when his volley came back off the crossbar, before Maierhofer's blushes were spared by an offside flag after he rolled the ball wide of an open goal.
Bournemouth had their moments as well, with Mark Beevers lucky to escape with a booking after tripping Ryan Fraser and Yann Kermorgant seeing the resulting free-kick turned round the post by David Forde.
But the goal Millwall craved arrived in the 29th minute when Scott Malone's curling cross from the left was met by a glancing header from Woolford.
Millwall hearts were in their mouths midway through the second half when Shaun MacDonald powered a header towards goal but Forde, named the Lions' player of the year before the match, showed why with a superb save at full stretch.
Simeon Jackson could twice have put the result beyond doubt when he was one-on-one with Camp but both times he rolled his shot wide, and Morison's header came back off a post.
Instead Millwall needed Forde to come up with saves from Andrew Surman and Tokelo Rantie towards the end as the jitters suddenly struck.
But the Lions held out and Holloway was able to celebrate mission accomplished as a raucous Den crowd invaded the pitch at the final whistle.