The tourists chose to retire out both openers Alastair Cook and Michael Carberry with 318 for none on the board, and then lost three more wickets for 34 runs before Joe Root (58no) saw them through to 430 for seven declared as this rain-ruined fixture moved towards an inevitable draw.
Root was required again, behind the stumps this time, when Prior had to stay off the field with a sore left calf as England gave their bowlers a chance of some overdue overs in the last session - and their hosts closed out the stalemate on a first-innings 119 for three.
Kevin Pietersen, Jonathan Trott and Gary Ballance were earlier dismissed in single figures in awkward batting conditions after the pitch had spent so long under cover.
As on day one, when Cook and Carberry batted well against the new ball and Australia A's seamers perhaps did not find a testing length quickly enough, there was sideways movement off the seam.
There was also variable bounce, and it was a combination of the two which cost Pietersen his wicket in his first innings of the tour.
He got off the mark with a clip off his legs off Trent Copeland and added an authoritative drive past mid off from Ben Cutting's last delivery before rain - which had already caused a delayed start - moved in again to restrict the morning session to just two overs.
But then in the first over after the resumption, pushing well forward and typically slightly round his pad, Pietersen was given no chance by a delivery from Copeland which nipped into him and kept devilishly low to see him off lbw.
Trott got a thin edge behind, pushing forward to a useful ball from Cutting, and then Ballance's miserable start to his England career continued.
Batting with his Yorkshire team-mate Root, the left-hander at least opened his account - unlike his two ducks from his two previous England innings to date - but cut a tense figure throughout a 17-ball stay which brought him four runs before he got stuck on the crease lbw to a Cutting.
Root was set up by a clutch of early deliveries in his favoured scoring area, behind square on the off side. But he had to work hard too, as did Prior - short of runs for much of this year and batting conservatively against type here to try get a foothold for the winter ahead.
Prior missed a sweep and was lbw to Jon Holland, and Stuart Broad hastened the teatime declaration when he was well-held by a diving Usman Khawaja at long on.
Broad sought clarification of the low catch as he made his way off, but appeared to stop short of anything more contentious at the start of a tour when he knows his on-field behaviour will be under the microscope among home crowds after his sometimes controversial Ashes summer.
Root had one moment of fortune, suriving a confident appeal for lbw by Cutting on 14, but was otherwise assured on his way to an 85-ball 50 as he demonstrated he is at home in the middle order as at the top - where England appear to have decided to deploy Carberry instead.
He appeared comfortable too when required to keep wicket, twice catching the ball via a deflection off James Anderson - first when the bowler snaked one through Alex Doolan's bat and pad and dislodged the off bail and then when Khawaja edged behind to go cheaply.
Doolan, a possible for an Ashes call-up, had impressed initially in making all but one of the 32 runs off the bat until he was dismissed.
That included three fours in one over from Broad which cost 18 in all, evidence that England's frontline seamer - who sat out last week's draw in Perth - will need more bowling before the first Test.
The same is doubtless true of Graeme Swann, although it was heartening for England's off-spinner that he took a wicket - pinning opener Michael Klinger lbw on the back foot with one that turned and kept low.