The on-loan Mexico international appeared to have been offside before he converted Steven Reid's cross but there was no flag and the Baggies escaped with a point which lifted them out of the Premier League's bottom three.
Midfielder Rory Delap's second goal of the season had put the hosts ahead in the 53rd minute in what had been an uninspiring game up to that point.
West Brom seemed to have undone all their hard work in hanging on in the early stages by switching off at a crucial time to allow the 34-year-old to take full advantage.
But in a spirited climax Roy Hodgson's side proved they have the appetite and spirit for a relegation fight and in truth they could have snatched the win as it was Stoke hanging on at the end.
Hodgson is still awaiting his first victory after taking two points from his first two matches since succeeding Roberto Di Matteo.
The criticism of the Italian was that his style was too open - Hodgson inherited the worst defensive record in the top flight - but old habits die hard and there remains plenty of work to be done if the Baggies are to survive with 10 matches remaining.
Hodgson tried to find a solution in the short term by bringing in the likes of Abdoulaye Meite for his first league appearance in nearly a year, setting up his team to cope with the physical battle he anticipated they would come under but the Baggies were keen to get their retaliation in first.
Striker Marc-Antoine Fortune escaped with no more punishment than a free-kick for flooring Danny Pugh with a leading arm but Youssuf Mulumbu gave referee Michael Oliver plenty of warning of his intentions, chasing back 40 yards to chop down Kenwyne Jones after losing possession to the striker, and was duly booked.
Jermaine Pennant forced a decent save from Scott Carson, making his first appearance since January 4, and the winger proved to be Stoke's main threat - Delap's long throw apart - in the first half.
But the closest he came to breaking the deadlock was just before the interval when he curled a free-kick on to the top of the angle of post and crossbar.
West Brom may have the top flight's leakiest defence but they regularly pose a threat in the final third.
Graham Dorrans and Fortune both tested Asmir Begovic with shots from the left and right of the penalty area respectively while Paul Scharner should have at least done the same just before the interval but bobbled a 16-yard volley wide.
There was little quality on show in the first half and after the interval glitches even crept into Delap's reliable delivery, with the midfielder throwing one effort straight out for a goal-kick.
Fortunately his close-range radar was unaffected and it was he who finally rose above the mediocrity - and Dorrans - to head home Pennant's 53rd-minute corner from three yards.
Delap's free header at the near post was symptomatic of the problems West Brom have experienced this season.
The goal finally injected some life into the game, with Brunt (twice) and Stoke's Jon Walters both worrying their opposing goalkeepers with shots from distance.
Begovic was the busier of the two goalkeepers, saving Dorrans' header with his legs after it deflected wickedly off Ryan Shawcross while watching helplessly as Fortune's looping header dropped onto the crossbar and over.
West Brom pressed for an equaliser but often they were guilty of trying too hard, with substitute Somen Tychoyi blazing well over from the edge of the penalty area.
But the visitors had a stroke of luck three minutes from time with their equaliser.
Reid swung in a right-wing cross and substitute Vela poked the ball past Begovic from close range despite appearing to have benefited from coming back from an offside position.
There was still enough time for Begovic to be required to make three crucial saves as West Brom sensed a late shock.
Vela proved you cannot write off West Brom with the chances they create but if they are to achieve top-flight survival it is the other end of the pitch they have to work on.