Poll, who according to newspaper reports will now step down from officiating, denied Niko Kranjcar's winner, initially giving the goal but, following severe protests from a number of Arsenal defenders, went back on his decision.
With Bolton and Reading both drawing, this would have meant a first-ever appearance in European football for the south coast side.
Portsmouth were therefore left to rue a case of missed opportunities as they faced an Arsenal side performing well below-par but failed to really break them down all afternoon.
Arsenal themselves missed out the opportunity to leapfrog above Liverpool in the Premiership table in what has been a disappointing season for Arsene Wenger's side.
From the outset the game had a distinct end-of-season feel about it.
Gael Clichy's deflected effort was acrobatically steered off the line by Djimi Traore and Julio Baptista was well denied by David James.
Apart from these efforts and a Sean Davis curler which narrowly missed the far corner, the sell-out crowd at Fratton Park had little to shout about.
Things though perked up momentarily when Emmanuel Eboue was sent sprawling under a clumsy challenge from Traore and Poll pointed immediately to the spot.
Baptista, hoping to earn himself a permanent deal with Arsenal in the summer, stepped up only to see his penalty gloriously tipped over the crossbar by James.
Pompey boss Harry Redknapp sent on Lomana Tresor LuaLua in the second half to inject more pace into the match and it was he who sparked yet another moment in the spotlight for Poll.
The Congolese striker dashed back on to his right foot and unleashed a drive which Mart Poom could only parry.
Richard Hughes dived in only to see his effort blocked by Philippe Senderos and, as Kranjcar slotted the ball into the empty net, the whole of Portsmouth began to celebrate.
Poll, though, after consulting his assistant, chalked the goal off and the cries of jubilation were soon replaced with groans of disappointment.