The frustration began to grow as Klasnic curled in a poor 20-yard effort which was easily cleared.
However, Megson defended the decision to take off Klasnic, who is on a season-long loan deal from Nantes.
It was a deserved if laboured victory for Bolton, whose evening was epitomised by the variable nature of Klasnic's contribution.
Ivan Klasnic, with five goals in his last nine matches, brought the first save out from Bunn following Tamir Cohen's cut-back.
During her campaign, Nrs Klasnic was careful to distance herself from her party's unpopular social and budget policies at the national level.
Klasnic scored his sixth goal in eight league matches in the first half before Kevin Davies made it 2-0 after 61 minutes.
Klasnic then directed a low 12-yard header so wide it almost went out for a throw-in before being collected by right-back Kyle Walker.
The home fans hit out at Megson after he took off goalscorer Ivan Klasnic, with Bolton leading fellow strugglers Hull 2-1 on Tuesday.
It marked a personal milestone for Klasnic, who has resurrected his career to become the first player to recover after having a kidney transplant.
Styria's governor, Waltraud Klasnic, a member of the People's Party, said her party's victory was a vote of confidence for the conservatives' policies in the region.
Then came the late goal drama with Rustu at fault as he unnecessarily dashed from his line allowing Modric to cross for Klasnic to head home neatly.
With 10 minutes to go, Bolton were denied a chance to register a presence on the scoreline as Ivan Klasnic's shot struck a post and skipped wide.
But Bolton never gave up hope and really should have equalised in the dying minutes when Elmander headed limply wide before Ivan Klasnic shot across the face of goal.
Bolton stepped up the pace and Ivan Klasnic curled his shot just wide before testing Burch from an acute angle and hooking a shot wide after being set up by Taylor.
If Bolton were to gain anything from the match they needed a quick response, but when substitute Ivan Klasnic fired over from inside the box the belief quickly drained from the visitors.
Poland's defense were given a boost with 17 minutes remaining when Bilic opted to replace the dangerous strike pairing of Klasnic and Mladen Petric, but that did little to help Leo Beenhakker's side at the other end of the field.
The goal involved two of the game's most impressive performers, with full-back Pranjic racing onto a loose ball on the edge of the Poland area before cutting a pass back to Klasnic, who slotted home first time low to Boruc's left.
Tottenham were frequently lackadaisical when Bolton were in possession, and both Matt Taylor and Ivan Klasnic should have punished early mistakes by Bale, whose impressive work on the overlap was on more than one occasion marred by a lack of defensive focus.
However, Bolton goalkeeper Jussi Jaaskelainen made several fine saves to prevent a rout, and Ivan Klasnic had the ball in United's net only for it to be ruled out before Matt Taylor reduced the deficit with 15 minutes left with a far-post header from a cross by Kevin Davies.
Croatia continued to push for the opener right up to the break and Jerko Leko sent a low 20-meter shot fizzing just wide of Boruc's right post, before the Polish number one did superbly to save from Klasnic on the stroke of half-time following another one-on-one with the Croatia hitman.
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