England lost two wickets in the final 30 minutes before tea to reach the end of the second session on 91-2.
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Root had been adjudged to have edged behind to Brad Haddin, but the decision was immediately reviewed with the batsmen insistent that he didn't clip the ball. The evidence on DRS and Hot Spot remained inconclusive, but the decision wasn't overturned and Root was forced to leave the pitch.
Cook, who remains unbeaten on 42, and Kevin Pietersen negotiated the final three overs before tea, but England must fight hard in the final session to retain a chance in this Test match.
You can keep track of the final session on day two by following Sports Mole's live commentary.