Donovan called time on his international involvement in the Connecticut friendly, with the USA's all-time leading scorer finishing with a remarkable 157 caps.
He was unable to add to his account of 57 US goals, though, agonisingly seeing a first-half effort hit the post.
Mikkel Diskerud looked to have given the US victory with his fifth-minute strike but Enner Valencia wrong-footed goalkeeper Brad Guzan with a 30-yard strike in the dying stages.
And Valencia's long-range effort - scored in the 88th minute - ensured both sides shared the spoils.
Donovan was the subject of a pre-match presentation, as he received a collage of all 14 US shirts he wore for the national team.
And he was involved early, helping set up Diskerud's early goal with a cross to Jozy Altidore at the back post.
Altidore passed to DeAndre Yedlin, and he quickly shifted the ball to Diskerud who calmly side-footed into the right corner.
Joseph Gyau limped off in the 15th minute with a left knee injury and was eventually replaced by Bobby Wood after emerging on crutches.
The hosts continued to dominate, though, as Altidore dragged a shot just wide before Donovan's moment came.
Altidore played the 32-year-old in and the crowd rose to its feet, only to see Donovan toe-poke an effort into the right post before the rebound frustratingly eluded him.
Ecuador fired a warning to the US with Guzan required to make three smart saves in a minute - twice to keep out Renato Ibarra - before Donovan poked wide in the 38th minute.
That was to be his last meaningful involvement as US coach Jurgen Klinsmann, as planned, replaced Donovan to a standing ovation.
Both sides struggled to find rhythm in the second half, although Wood fired over in the 66th minute.
Ecuador grew into the game as it went on and Valencia delivered their sucker-punch with a bizarre goal.
The West Ham forward's strike swerved in the air and left Guzan stranded to deflate the home crowd.
The US still could have won, though, after a mix-up in Ecuador's defence played Wood in during the fourth minute of stoppage time.
But Wood - in two minds whether to short or square to Chris Wondolowski - saw his attempted cross cleared, meaning Klinsmann's men had to be content with a draw.
