Strauss, who was dropped from the England side and took up a short-term contract with New Zealand first-class side Northern Districts to play himself back into form, was 55 not out with his team 155 for three when bad light forced players off the field.
Pietersen, who scored 50 in the first innings, was caught by Bevan Griggs off Mark Orchard for 53, which included five boundaries and three sixes, while Ian Bell was 21 not out.
The tourists hold a 15-run lead with seven wickets in hand after Steve Harmison had taken four quick wickets to help bowl the Selection side out for 271 and a lead of 140.
The Selection team captain Jamie How top-scored with 65, while there were useful contributions from fellow Test hopefuls Matthew Bell (40) and Mathew Sinclair (47) at the University Oval.
After a 90-minute delay due to rain, the Selection side resumed on 177/4 but lost regular wickets with fast bowler Harmison the major destroyer, picking up four wickets for 41, to finish the innings with 5/100 from 22 overs.
"I've got marginally better the more and more I bowled," Harmison told reporters. "I'm still trying to find my feet and find a length on these wickets.
"I'm the sort of bowler that takes time to being in a different country. I've been here for eight days, I'm reasonably happy."
England's second innings began poorly with Michael Vaughan (13) and Alastair Cook (12) both dismissed cheaply to leave them struggling at 27-2 in the ninth over before Strauss and Pietersen combined for a 90-run partnership.
The hosts New Zealand take on England in the first of the three-Test series in Hamilton starting next Wednesday.
Brief Scores (D-2):
England 131&155/3 (Andrew Strauss 55 n o, Pietersen 53, Ian Bell 21 n o; Orchard 1 for 16, Mark Gillespie 1 for 30) Vs NZ Selection XI 271 (Jamie How 65, Matt Sinclair 47, Matt Bell 40; Harmison 5 for 100, Panesar 2 for 27).