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An outstanding performance from stand-in goalkeeper Sorin Colceag almost earned the home side a deserved point, despite conceding a lot of late possession, but Shearer's spot-kick on 87 minutes broke Greek hearts.
With Patrick Kluivert injured, Newcastle coach Graeme Souness started with Craig Bellamy in attack alongside Shearer. Panionios, meanwhile, were missing their first-choice goalkeeper Jaroslav Drobný, although his replacement appeared a capable deputy from the off.
The Romanian goalkeeper seemed thoroughly unflappable, coming off his line to avert the threat of the pacy Bellamy and saving well from Laurent Robert and Jermaine Jenas. But it was his opposite number Shay Given who had to deal with the best effort of the first half, stretching to his right to palm away Mário Breška's glancing header on 23 minutes.
Neither side settled well on the bumpy pitch's long grass, but Newcastle's frustration was more evident than their hosts', Stephen Carr's booking the culmination of a series of niggly fouls by his Newcastle team-mates as they failed to find any sort of shape or rhythm despite dominating possession.
The hosts set about their task with discipline, keeping the ball on the move and their opponents under pressure. Nevertheless, they always seemed one mistake away from allowing Newcastle a sight of goal, and Colceag was relieved to see Jenas scoop over after his poor punch right on half-time.
Newcastle up pace
The visitors began the second half in a more upbeat fashion, Robert getting to the by-line on three occasions in the first ten minutes. However, it was not until after the hour mark that Colceag was again called into action, saving at Bellamy's feet.
As Newcastle turned up the pressure on their opponents, the promise of the first half deserted Panionios as they struggled to gain possession. Colceag was increasingly busy, and on 76 minutes he pulled off the save of the game, tipping over from Shearer's seven-metre header.
After several further saves and parries, most notably from another Robert drive, it seemed the 32-year-old stand-in keeper was to be the home side's hero. But with just three minutes remaining Euripidis-Grigorios Makos felled substitute Shola Ameobi, and Shearer drove in from the spot to claim his fourth goal of this season's competition.
The win extends Newcastle's unbeaten run under new manager Souness to eight games. For Panionios, though, it is four defeats in five. The Greek side next travel to Sporting Clube de Portugal on 4 November, while Newcastle take on FC Dinamo Tbilisi at home on the same night.
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