Lennon had guided Wanderers to their first away victory of the season at Birmingham on Saturday while Charlton’s unbeaten record was ended by Bournemouth.
But normal service was resumed as goals from George Tucudean and Johnnie Jackson got the Addicks back to winning ways despite Dean Moxey pulling one back for the visitors, who remain in the bottom three.
Nevertheless, Lennon has clearly made an impact since replacing Dougie Freedman, and his new side were the better team for long periods.
The former Celtic manager also clearly had not learned his lesson from Saturday, when he was sent to the stands for persistently leaving his technical area, as he raced down the touchline to protest against an offside decision shortly after Tucudean struck.
Bolton, looking far more confident than they ever seemed to under Freedman, created the better early chances with Lee Chung-yong and Jermaine Beckford forcing saves from home keeper Stephen Henderson.
But Charlton scored with their first clear-cut opportunity in the 27th minute when Yoni Buyons spotted Tucudean’s run behind the Bolton back four and found the Romanian with a clever ball over the top.
Tucudean still had plenty to do, but he brought the ball down superbly before striding towards goal and tucking it past Andy Lonergan for his second goal of the season.
Bolton pushed for an equaliser before half-time and former Charlton defender Dorian Dervite headed narrowly over from a corner before Beckford took an air shot in front of goal.
But the Addicks made it to the break in front and then doubled their lead five minutes after the restart when Tucudean squared the ball for skipper Jackson to slot home from 15 yards.
However, within three minutes Bolton had halved the arrears when Charlton cleared a corner only as far as Moxey on the edge of the area, and the left-back crashed a superb low drive past Henderson and into the corner of the net.
Urged on by Lennon, Bolton again went in search of a leveller and they came agonisingly close when Dervite’s header was cleared from underneath the crossbar by Rhoys Wiggins.
But they could not find a way past a resolute Charlton, who weathered the late storm and dealt Lennon his first taste of defeat with the Trotters.