After winning the toss, England would have hoped to put themselves into a commanding position at Old Trafford but each of their top order failed to put together a lengthy knock.
Keaton Jennings was the first to be dismissed for 17, and although England made it to lunch with nine wickets intact, it was not long before Alastair Cook (46) and Tom Westley (29) fell in quick succession.
England needed an innings from skipper Root and although he made yet another fifty, he went for 52 soon after Dawid Malan had made just 18.
Stokes needed to find a balance between defence and attack during the third session but after making 58 from 96 deliveries, he was dismissed with just six balls of the day remaining.
Jonny Bairstow remains at the crease unbeaten on 33, but he will probably have to bat through to the end of the innings for England to post a total close to what they had hoped for at the start of the day.