The defeat was not the only bad news for Karel Freye. Influential skipper, Johnnie Jackson, had to go off with a hamstring injury after only 13 minutes.
Fraeye went with the same starting XI as he used at Birmingham, with Tareiq Holmes-Dennis confining fit-again Chris Solly on the bench.
Holmes-Dennis was pushed into midfield when Solly came on as an early replacement for Jackson.
Ipswich took the lead through a scrappy goal just before the half-hour mark. Stephen Henderson made a smart save but Charlton failed to clear their lines. The ball ping-ponged around before Daryl Murphy nodded it past Henderson.
The Tractor Boys doubled their advantage in stoppage time. A hopeful ball into the box fell kindly for Freddie Sears, who steered inside Henderson’s near post.
There was still time for the Addicks to have an attack scrambled away, and Morgan Fox picked up a booking for hauling Ainsley Maitland-Niles down.
Ricardo Vaz Te replaced Fox at the start of the second period, as Fraeye looked to increase his attacking options.
A neat move midway through the half, gave Murphy the chance to seal the game for Ipswich. He shot across Henderson and the ball crossed the line just inside the far post.
Dean Gerken was called upon to make a number of smart saves to twice foil Vaz Te, and deny Patrick Bauer as well.
The defeat was not at all what Charlton needed, with a tough trips to Brighton and Burnley coming up before Christmas.
Christmas cheer is likely to be in short supply at The Valley this year.
Charlton: Henderson, Solly, Bauer, Sarr, Fox (Vaz Te 46); Diarra, Cousins, Jackson (Solly 13), Gudmundsson; Makienok (Ghoochannehad 73), Lookman.
Subs (not used): Pope, Lennon, Ahearne-Grant.
Booked: Fox 45(foul), Makienok 63 (foul).
Ipswich: Gerken; Knudsen, Smith, Berra, Chambers; Maitland-Niles (Coke 84), Skuse, Douglas,Sears (Oar 90); Murphy, Pitman.
Subs (not used): Bialkowski, Parr, Tabb, Malarczyk, Robinson.
Goals: Murphy 28, 68 Sears 45.
Referee: Scott Duncan (Northumberland).
Attn: 15,870 (2,678 Ipswich).