After going so close to guiding Wales to Euro 2004, Hughes' tenure has ended on a downbeat note with his side now unlikely to qualify for the World Cup in 2006 after taking just two points from their first four Group Six matches.
Wales were without Ryan Giggs who had a stomach bug so Hughes partnered Rob Earnshaw with Craig Bellamy up front, while John Hartson was dropped to the substitute's bench.
Robbie Savage returned to add some bite to the midfield and it was Wales who started brightly with Earnshaw latching on to a poor back header by Jacek Bak in the seventh minute, before blasting his shot wide.
Earnshaw was sent clear again in the 18th minute and he fed Mark Delaney, whose cross was gathered at the second attempt by Jerzy Dudek.
When Wales attacked again Earnshaw just failed to get on the end of Delaney's cross before Dudek touched Bellamy's fierce 30th minute shot on to the outside of a post.
Dudek then tipped Simon Davies' 20-yards shot over the bar as Wales ended the first half on top.
Hughes' side continued where they had let off as the second period started andBellamy and Davies both fired over the crossbar.
It came as no surprise when Wales finally broke the deadlock in the 55th minute.
A quick free-kick by Savage sent Earnshaw free and he beat Tomasz Hajto before clipping a shot over Dudek.
Poland almost equalised immediately when substitute Tomasz Frankowski hooked a shot over the bar before Dudek did well to keep out Bellamy's header at the other end.
The Poles grabbed an equaliser with 19 minutes left when Frankowski took advantage of indecision between Danny Gabbidon and James Collins to shoot past Paul Jones.
The goal seemed to knock the stuffing out of Wales and the Poles took the lead in the 81st minute after a swift counter-attack.
Frankowski found Maciej Zurawski who ran into the penalty area before drilling a shot high into the net.
Worse was to come for Wales four minutes later when the Poles made it 3-1.
This time Jacek Krzynowek tried his luck from 25 yards out and the ball sailed past the unfortunate Jones.
With virtually the last action of the game Hartson headed home but it was too little too late for the Welsh.