Full-time from The Den
A 32nd-minute penalty from Yann Kermorgant put The Cherries ahead before Harry Arter fired home a second - his fifth goal in successive games - three minutes before the break.
Any hope The Lions had of repeating the dramatic fightback of last month at the Goldsands Stadium, when late goals from Ed Upson and Magaye Gueye secured a 2-2 draw, disappeared when Shaun Williams was shown a straight red card with 11 minutes remaining for retaliation after being thrown to the ground by Callum Wilson.
Along with Nelson, Andy Wilkinson and Scott Malone returned to a new-look defence with Jimmy Abdou, Scott McDonald, Martyn Woolford and Lee Gregory also in the starting XI.
For centre half Nelson, it was certainly a baptism of fire against a free-scoring Cherries side that have averaged over 2.26 goals per game this season.
Little could Nelson have expected to start the game at centre half, play a chunk of the second-half at right-back before ending up as the lone central defender for the last 11 minutes following Williams' dismissal.
The positive performance of Nelson, who turns 19 on 1st January, was one of the plus points on an afternoon that saw Millwall slide to their fourth successive defeat at The Den, and remain just three points above the dreaded drop zone but having played a game more than Wigan and Brighton.
Holloway brought on Ricardo Fuller at the start of the second-half and The Lions had a great chance to reduce the deficit 10 minutes after the break when Gregory was a whisker away from connecting with Abdou's deft dinked through ball. A goal then would undoubtedly have breathed some much needed belief into both the team and home supporters, who did their best to get behind the team throughout.
Former Lions loanee Adam Smith could have put Bournemouth 3-0 ahead on 59 minutes, but an excellent block from Nelson averted the danger.
Sub Dan Gosling drilled a 16-yarder wide of the left hand post and Wilson guided a header straight into the hands of keeper Forde as Howe's men continued to ask questions of the home defence.
Despite showing plenty of determination against the south coast outfit that will surely be in the promotion shake-up come May, The Lions hopes of clawing their way back were shattered when Williams was red-carded for his retaliation to Wilson's reaction following his initial foul, which earned the Cherries' striker a yellow card.
There was to be no way back with Millwall's best chance late on when Magaye Gueye and Fuller broke clear, initially in a two on one situation, but the Cherries were so quick to regroup within seconds they had eight men behind the ball and the opportunity was lost.
Bookings: Shittu (12mins), Forde (34mins), Wilkinson (45+1min), McDonald (61mins)
Sending off: Williams (79mins)
AFC Bournemouth: Boruc, Francis, Elphick, Cook, Daniels, Ritchie (Fraser, 88mins), Arter, Surman, Smith (Pugh, 69mins), Wilson, Kermorgant (Gosling, 58mins). Subs not used: Camp, Cargill, Pitman, Rantie.
Bookings: Surman (33mins), Smith (51mins), Wilson (79mins)
Scorers: Kermorgant (32mins, pen), Arter (42mins)
Ref: D Coote
Att: 10,407 (away 1,278)