A troublesome left leg and a fresh problem in his right shoulder failed to deter the England captain, who snared KL Rahul for 90 on the last morning of the fourth Test to give his side hope of moving into an unassailable 3-1 series lead.
Jofra Archer then dismissed Shubman Gill for 103 on the stroke of lunch but Joe Root dropping Ravindra Jadeja from the next ball proved crucial as he and Washington Sundar batted out the rest of the day.
However, there were farcical scenes at the finish on Sunday when it became clear there would be no winner as India's batters elected against shaking hands with 15 overs left - the earliest opportunity a draw could be agreed - so both could get their hundreds.
Root and Harry Brook provided buffet bowling to speed things along, with Jadeja getting to his ton first and and Sundar followed to signal the end of proceedings, with India on 4-424 and a lead of 113.
With the fifth Test getting under way on Thursday, much of the focus will likely centre on Stokes' availability after he was left weary and wounded in Manchester.
He battled cramp in his left leg when batting on Friday and reported general soreness on Saturday, which meant he did not bowl as Rahul and Gill took India from 2-0 to 2-174 overnight.
Stokes returned to the fray on the final morning and made the breakthrough with his 20th delivery. Rahul was beaten by a nip-backer that thudded into his knee roll in front of middle stump.
Having moved on to a titanic 700 runs for the series, Gill brought up a fourth three-figure score of the trip off 228 balls with a push into the offside for a single.
By then, England had the second new ball, taken 40 minutes before lunch, and Archer claimed the prize wicket of Gill.
Root parried then dropped the rebound at head height after Jadeja flirted at a rising delivery from Archer first up.
With the pitch flattening out, Sundar and Jadeja grew increasingly confident through the afternoon.
Both teams must agree on the draw and England were clearly unhappy at the pair continuing, with Brook eventually called upon to send down some floaty off-spin while Root was kept on.
Jadeja got to his hundred in a blizzard of boundaries, eventually finishing on 107 not out, before Washington brought up his first Test century in Brook's next over before hands were shaken five overs after England had first offered them.
Stokes said: "I'll always try and give everything that I possibly can. Try and run through a brick wall.
"I ask the guys up there to run through a brick wall for the team. I'll always try and do the same to try and lead by example in that sense.
"Bowling, being out in the field all that kind of stuff it is tough work, but pretty sore."
Asked about his shoulder, he added: "It's just a workload thing, got through a fair few amount of overs and just everything starts creeping up on you.
"I'll keep trying, keep going. As I always say to all the bowlers, pain is only an emotion."
India have their own injury issues for the final Test with coach Gautam Gambhir revealing that Rishabh Pant, who was taken from the field on a cart on the first day, is ruled out with a foot fracture.
