Eddie Howe’s Cherries played for 54 minutes with 10 men after Yann Kermorgant was shown a red card for a chest-high tackle on Mark Davies.
Despite the man advantage Wanderers struggled for large parts to make it count.
Even when skipper Jay Spearing cancelled out Wilson’s first goal with a deflected left-footed effort from outside the area, there was no real spark from the home side.
And they paid the penalty for their lethargy when Wilson escaped Matt Mills and Dorian Dervite to tuck away his second of the afternoon after 68 minutes.
To add injury to insult Bolton also lost injury jinxed midfielder Mark Davies to a first-half knee problem.
Bolton have now lost five successive league and cup games and are in a major fight to save their Sky Bet Championship status once the season resumes after the international break.
Freedman parted company with the club on Friday morning after nearly two years and 99 games in charge but was convinced 24 hours earlier he would still be at the helm to reach three figures.
Wanderers then refused to confirm who would take temporary charge, hinting it would be Under-21s boss Jamie Fullarton and player-coach Andy Hughes.
In the end, they plumped for Hughes and goalkeeping coach Lee Turner.
Notable by his absence from the temporary management team is former Trotters favourite Jimmy Phillips, who was handed the caretaker role prior to Freedman succeeding Owen Coyle.
That snub suggests Phillips will also be out of the running when chairman Phil Gartside draws up a shortlist that will almost certainly include former Watford and Cardiff manager Malky Mackay.
Wanderers’ long serving chairman continues to be a hate figure for a small section of the home support who gathered outside the main entrance prior to kick-off, shouting abuse and waving banners.
Inside, the reception for the team was far more harmonious than it had been a week earlier following a 2-0 defeat to Derby.
And the first post Freedman line-up noticeably omitted two of his former Palace players – Dean Moxey and Owen Garvan.
And they started brightly as Craig Davies tested Artur Boruc after just 12 seconds.
Davies and Jermaine Beckford squandered other chances before the visitors began to pepper Andy Lonergan’s goal with a succession of shots and were unlucky when Dervite cleared one effort from under his crossbar.
But Kermorgant’s dismissal appeared to have tipped the balance of the game Bolton’s way.
Instead, all the old failings were still too apparent with chances squandered in attack and poor defending allowing Wilson his expertly taken brace.
He struck for the first time just after half-time, cutting into the area and finishing low past Lonergan.
And it was against the run of play when captain Spearing let fly from outside the area, his left-footed effort taking a deflection past Boruc.
Instead of going on to claim only their second league win of the campaign, Wanderers allowed Wilson to break clear and add his second goal.
Bolton huffed and puffed but rarely threatened a second equaliser and there were predictable calls for Gartside to resign after final whistle.