The Frenchman paced the technical area two days after coming to England to begin a new career as Pompey's latest manager and could hardly have expected a better start, with his new side taking the lead in the third minute.
Lomana LuaLua made an opening for Steve Stone whose centre from the right gave Yakubu Ayegbeni a free header for his 15th of the season.
Charlton, still eyeing a UEFA Cup place, saw Danny Murphy booked after 14 minutes and then lost Radostin Kishishev with a facial injury after 19 minutes.
His replacement, Jerome Thomas' first contribution was to give away a foul from which Patrik Berger floated in a free-kick that Stone glanced home.
At this stage Portsmouth looked comfortable and Charlton were in some disarray, but the visitors were thrown a lifeline two minutes later.
Charlton were awarded a free-kick on the left, Murphy took it quickly and big defender Jonathan Fortune rose to head in.
Hermann Hreidarsson was booked for a foul on Stone just before the break and then in first half injury-time the Addicks pulled level.
Thomas was brought down on the edge of the area and Murphy stepped up to bend a free-kick beyond the defensive wall and past a static Jamie Ashdown.
The second half could have gone either way with Yakubu blazing over the bar wastefully from 12 yards and Shaun Bartlett blocking a shot on the line from Giannis Skopelitis.
Yakubu hit the post in the 65th minute and then Ashdown made up for his part in Charlton's second by making an excellent save from another quickly-taken free-kick by Murphy.
As the match appeared to be drifting towards a draw Portsmouth scored twice in the last eight minutes.
In the 82nd minute LuaLua crossed from the right corner flag and substitute Diomansy Kamara stole in ahead of the goalkeeper to score with a stunning header.
In injury-time and with Charlton committed to attack in search of an equaliser, Yakubu played a perfect pass for LuaLua to run on and beat Kiely with a low shot.
Man of the Match: Lomana LuaLua - The livewire striker caused problems for the Charlton defence all afternoon and sealed a vital win with a well-deserved last-minute goal.