England's under-pressure captain was bowled off his thigh pad for five as his side closed on 43-1 in reply to India's 457, which included a 111 partnership between Bhuvneshwar Kumar and number 11 Mohammed Shami - a record for a last-wicket partnership for India against England.
After watching India post a healthy total on a bat-friendly pitch, Cook arrived at the crease determined to shake off his poor run, but his luck refused to change as for the 25th test innings in succession he failed to reach three figures.
Looking nervous from the first ball, Cook was a little unlucky when he moved across his crease and Shami's delivery deflected off his thigh pad on to the stumps.
Sam Robson (20) and Gary Balance (15) got England through to stumps without many more alarms.
England had prospered earlier in the day, taking five wickets either side of lunch to reduce India to just 346-9 after the visitors had begun the day well placed on 259-4.
India were cruising towards the 500 barrier when they reached 342-5 for five at lunch with Murali Vijay having earlier been out for 146 and captain Mahendra Singh Dhoni 81 not out.
Two wickets for Ben Stokes, one for Stuart Broad and a brilliant run out by James Anderson shortly after the interval threatened to ruin India's day.
It was a surprising turn of events on a flat and slow pitch that has drawn widespread criticism and led to claims it had been designed to ensure the match goes the distance in order to maximise revenue, an accusation dismissed by Nottinghamshire's chief executive.
"The idea that as a chief executive I would put pressure on to produce any sort of pitch is a bit silly actually," Lisa Pursehouse was quoted as saying by the BBC.
The pitch, however, meant opportunities were few and far between for the hosts' bowlers but their patience paid off in a blistering spell at the start of the afternoon session as India lost four wickets for two runs.
Stokes, who had little reward for his efforts in the previous sessions, struck in the second over after the interval when Ravindra Jadeja (25) recklessly swung at a ball outside off stump and was caught behind by Matt Prior.
Dhoni fell soon after when he attempted to steal a needless single and was brilliantly run out by Anderson, who caught the batsman marginally out of his crease with a direct hit.
Four balls later debutant Stuart Binny drove at a Stokes delivery and found the grateful hands of Joe Root.
Right-arm seamer Broad wasted no time in getting in on the act when he clattered the ball into Ishant Sharma's stumps.
Any hope that England would finish off India quickly disappeared though as Kumar and Shami batted superbly to add more than 100 runs to the total, both registering their first test fifties.
Spinner Moeen Ali, who had been targeted by India's batsmen, finally made the breakthrough when Kumar chipped straight to Root at mid-on to end their innings.
The day had started well for the tourists and Vijay looked to be on his way to his third test 150 but fell to a marginal lbw decision off Anderson, ending a 126-run fifth-wicket stand with his captain.
Replays showed the ball was bouncing over the stumps but with the series being played without the aid of the decision review system - India refused to use it - the wicket could not be challenged.
- Sports & Recreation
- Bhuvneshwar Kumar
- Mohammed Shami
- James Anderson