Plucky Walsall worked hard and despite being battered at times, they pushed the hosts right up until the final whistle.
In a poor first half the person most in the spotlight was referee Paul Taylor, who cautioned five players, most for fairly minor offences.
Counago and Jamie Clapham, twice each, sent efforts wide for Town, while Darren Wrack volleyed the Saddlers' only opening well over.
Tommy Miller had a shot blocked on the line after, before Counago tapped home in stoppage time after keeper Gavin Ward spilled Richard Naylor's low cross.
The second half, by contrast, was action all the way, as Town came out firing only to miss good chances as Naylor headed a Jim Magilton cross straight at Ward and Magilton himself blazed a Counago cross over.
Ipswich finally got their second goal on the hour when Thomas Gaardsoe glanced home Magilton's corner for his third goal of the week - all headers.
Both sides had penalty shouts rejected before Fitzroy Simpson got in the way of a goal bound Magilton drive from another Counago lay off.
Out of nothing, Walsall got a goal back after 68 minutes when Wrack arrived to slide home Zigor Aranalde's low cross.
Town rallied and Ward saved from Counago and Clapham, before Andy Marshall made the save of the game to tip over a fierce Wrack volley.
Counago got his 13th of the season five minutes from time with an angled shot, but still Town were not safe as Wrack bundled in Darren Bazeley's curling cross.
Right at the death Walsall could have snatched a point when Bazeley's goal bound shot rebounded away in a crowded penalty area.