Andy Keogh grabbed his sixth goal of the season - and his first of 2013 - as The Lions battled for an excellent point in their first-ever visit to the Reebok Stadium.
Keogh took just nine minutes to mark his return to first-team action confidently converting a penalty after he had been fouled by Zat Knight.
But Bolton hauled themselves level with the second spot-kick if the game, Keith Andrews slamming home after Lee had been fouled by Danny Shittu.
Both teams had opportunities to take all three points, but in the end a draw was just about the right result.
"We battled very well and we defended when we needed to," said Millwall boss Kenny Jackett.
"In the first half we caused quite a few problems going forward and in the second half, it was much more of a rearguard action from us, certainly in the opening 20 minutes.
We seemed to come through it and came on strong ourselves; it was a hard earned point but a well deserved one.
Overall we've got four points out of six from a Bolton team that were in the Premiership last season and this result keeps us in touch, where we want to be."
Lions boss Jackett made four changes to his starting line-up, handing a debut to new signing Martyn Woolford and welcoming fit-again trio of Shittu, Liam Trotter and Keogh back into the team.
Woolford, signed from Bristol City on Wednesday, filled the left midfield berth with Shittu stepping in to the heart of defence, Trotter replacing Josh Wright in the engine room and Keogh starting alongside Dany N'Guessan up front with Darius Henderson dropping to the bench.
Bolton posed an early threat when David Ngog sped down the left flank and despatched an inviting delivery that flashed across the face of goal and away from the boot of Kevin Davies, waiting to pounce.
However, it was The Lions who went ahead on nine minutes courtesy of Keogh's penalty. A poor ball from Tim Ream caught Keith Andrews on his heels, and N'Guessan slipped the ball through to Keogh, who was tripped by the retreating Zat Knight.
Keogh nonchalantly dinked the resulting spot-kick down the middle to spark wild celebrations from the 1,200 travelling fans.
Millwall looked crisp and controlled in their attacking play and for the following 20 minutes were in total control, doing everything except increase their goal tally.
A stunning long-range piledriver by Trotter flew a foot wide of the mark whilst home keeper Adam Bogdan made a smart save from N'Guessan's stinging 18-yarder and Woolford's goalbound drive was deflected wide for a corner.
A fantastic passage of play midway through the half involving Trotter and Adam Smith so nearly produced a second goal that, at that stage, the visitors performance deserved, but Henry was unlucky not to put the icing on the cake as his sweet left foot drive whistled narrowly wide.
Millwall were rocked, however, nine minutes before the break when Bolton were handed a lifeline against the run of play.
Lee drew a clumsy challenge from Shittu and Keith Andrews sent Lions keeper David Forde the wrong way as the teams went in level at the break.
After such a lethargic opening 45 minutes, the home side came out all guns blazing and upped their effort and tempo.
"The commitment was there," said Trotters boss Dougie Freedman, "And that was pleasing after such a poor start.
We came out at the start of the second half and tried to get at them and gave it everything that we had.
We made some bad decisions in the final third and maybe could have won the game."
Freedman's men certainly turned the screw after the break with Marcos Alonso and Ngog forcing excellent saves from Forde in the Millwall goal.
But the visitors, inspired by man of the match Trotter, dug in and defended in numbers whilst posing a real threat on the counter-attack.
A sublime ball from Henry was a whisker away from the boot of N'Guessan, who had stolen in unmarked at the far post, as The Lions came within inches of edging ahead in the final 10 minutes.
And N'Guessan was involved at the other end, making a vital goal-line clearance in the dying moments to head Davies' effort off the line.
Bolton Wanderers: Bogdan, Ricketts, Knight, Ream, Alonso, Spearing, Andrews, Eagles (Sordell, 80mins), Chung-Yong (Afobe, 71mins), K Davies, Ngog. Subs not used: Lonergan, Mears, Pratley, Eaves, Vela.
Booking: Alonso (88mins)
Scorer: Andrews (34mins, pen)
Millwall: Forde, A.Smith, Lowry, Abdou, Shittu, Beevers, Woolford, Trotter, Keogh (Henderson, 79mins), N'Guessan, Henry. Subs not used: M.Taylor, J.Smith, Wright, Batt, Osborne, Marquis.
Bookings: Lowry (63mins), Forde (84mins)
Scorer: Keogh (9mins, pen)
Att: 16,985 (away 1,162)