"I think he has broken his nose," said England captain Alastair Cook, who added that Broad had been taken to hospital. "He had a nasty blow but I think he'll be all right."
England had established a 215-run lead going into the second innings after overnight pair Joe Root (77) and Jos Buttler (70) pushed their seventh-wicket partnership to 134.
Some lusty blows from the tail took the total to 367 - Broad (12) didn't reappear - and meant a draw was likely to be the best India could hope for.
Surviving until stumps was the order of the day but after reaching tea at 33-1, India's fragile batting lineup disintegrated in face of some fine spin bowling by Ali, who found pace and bounce on a good Old Trafford wicket.
The last nine wickets fell in around two hours, even with Broad absent and James Anderson feeling ill and only bowling nine overs.
"We knew we had to have a big effort in that three hours," said Cook, whose position was under threat when India was 1-0 up after two tests of the series.
On Ali, an allrounder playing in his just his sixth test, Cook added: "I have never seen a bloke work so hard and make such an improvement in a short space of time."
India was bowled out for 152 in the first innings in the face of some brilliant swing bowling by Broad and Anderson. The tourists' two innings lasted a total of 89.4 overs.
"The batting department is definitely something we will have to improve in the fifth test," India captain Mahendra Singh Dhoni said. "Maybe a few of them are going through a lean patch all together."
When Virat Kohli edged Anderson to second slip to be out for 7, leaving his average for the series at 13.5, India had lost four wickets for just eight runs in 23 balls and were reeling on 61-5.
Only Ravichandran Ashwin (46 not out) offered any real resistance in the lower order.
- AP