Shoaib Akhtar and Mohammad Asif bowled well in helpful conditions to take two wickets each in a game cut to 40 overs. Andrew Strauss edged Shoaib behind for a golden duck after the start was put back by 90 minutes because of drizzle.
After another shower Marcus Trescothick and Ian Bell drove to slip and Kevin Pietersen miscued a heave off Asif.
Earlier in the day Pakistan won the toss and chose to bowl first in the rain-delayed match at Lord's.
England announced one change to their team from the first match, which was washed out at Cardiff last Wednesday, bringing in Jon Lewis for fellow seam bowler Sajid Mahmood.
Pakistan were again unchanged from the team that won the Twenty20 International and played at Cardiff.