The League Two outfit rocked their hosts inside just 13 seconds, when Joel Grant curled an exquisite shot beyond Pompey keeper Simon Eastwood.
Chairboys' Jo Kuffour wriggled his way through the Portsmouth defence before firing against the foot of the post after eight minutes.
He then had two attempts blocked in a desperate goalmouth scramble a minute later, before Morgan doubled Wycombe's advantage.
Kuffour rattled the Pompey upright again after 17 minutes, before the contest threatened to fizzle out.
That was until a cross from Pompey's Wes Thomas caused havoc in the Wycombe box and Izale McLeod pulled one back for Michael Appleton's men two minutes into first-half stoppage time.
Wycombe extended their lead after 55 minutes, when Bruno Andrade won his side a penalty after being felled by Adam Webster.
Eastwood saved Morgan's spot kick brilliantly to his right, but the Chairboy stooped to head in the rebound.