Chasing England's first innings total of 589-8 declared, the visitors were left at 57-4 overnight, a huge 532 behind the hosts.
With this double century, Root became the first England batsman to hit a double-century against Pakistan in a home Test since Denis Compton's 278 at Trent Bridge in 1954.
Misbah-ul-Haq, the Pakistan captain, top-scored for his side with 52 and shared a ninth-wicket stand of 60 with Wahab Riaz, who made a Test-best 39.
Root added: "Today we played a lot straighter".
Hungry England should have faced a tough slog to claim 20 wickets on this batsman friendly pitch but having gone 1-0 down in the first Test they have already bitten a sizeable chunk out of the Pakistani batting.
And England assistant coach Paul Farbrace believes the decision to bat again was the correct one and hopes that will be proved with a win to level the series.
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They finished on 98 for one, with Hales falling to Mohammed Amir, with England 489 runs ahead at stumps.
After winning the first test last week, Pakistan found themselves in a awful position on day three at Old Trafford.
That gave Shah then-innings figures of one for 139 in 38.4 overs - a marked contrast to his man-of-the-match return of 10 for 141 during Pakistan's 75-run win in the first Test at Lord's last week.
Rain forced the players off the field for about an hour and when they returned Asad Shafiq, on four, drove loosely at a wide ball from Stuart Broad and Alex Hales took a simple catch at point.
After putting on a 185-run stand for the second wicket with skipper Alastair Cook on the opening day, he further consolidated England's position in the match with his show on Day 2.
Cook had the opportunity to put Pakistan back in again once England bowled the tourists out for just 198.
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Sarfraz Ahmed may have come in at 76 for six but the wicket-keeper stuck to his attacking game and got off the mark when he cut Broad over Hales's head for four.
With Pakistan given 24 overs to bat, England hit back emphatically as Woakes grabbed two wickets before the returning Stokes got his first. "We thought we'd bat while the wicket was still good, rather than put ourselves under pressure when it gets worse".
So too were England, after Stokes had an out-of-sorts Younus caught down the leg-side and then Woakes himself found a short ball too good for an authentic but unsuccessful nightwatchman in Rahat.
Wahab hoisted Ali for six. Sarfraz's 26 featured five fours but Pakistan were now 112 for 7.
Mohammad Amir, another of Pakistan's left-arm quicks, was uppercut for six high over third man by Woakes.
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