Watkins replaced him 10 minutes earlier after another below-par display, but the Three Lions captain was among the players to rush the pitch after the last-gasp goal.
Despite his underwhelming showing, Kane equalised from the penalty spot in the first half, becoming the joint-leader in the Golden Boot race.
The 30-year-old has now scored three goals at Euro 2024, a tally only matched by Spain's Dani Olmo among players in Sunday's final.
But he will have been disappointed to be hauled off with the game finely poised at 1-1 as Gareth Southgate called on Watkins to make the desired impact.
And did he?! The Aston Villa striker latched onto Cole Palmer's through ball before firing low and hard across Bart Verbruggen from a tight angle, blowing the metaphorical roof off the Westfalenstadion.
As Watkins wheeled off towards the corner flag, England's bench, including Kane, couldn't help but stream onto the pitch in pure jubilation.
Southgate's players surrounded the match-winner in an emotional huddle, knowing many of them would be in for the game of their lives in four days' time.
England players celebrated Ollie Watkins' winner together. (Image: Getty)
The Three Lions are among the favourites to win this summer's Euro 2024 tournament and you can get your hands on the brand new Nike home and away kits before the first whistle.
After full-time, Watkins talked through his winner, explaining that he didn't think he had struck a ball as well in his entire career.
He said: "The ball came into me; hold up is not the strongest side of my game, but the goal was my bread and butter.
"I said to Cole Palmer we were both going to go on the pitch, and he would set me up, and it happened.
"You don't get that opportunity very often and I had to be greedy and take the shot. I don't think I have hit the ball so sweet like that before."
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Kane was among those hailing Watkins after the final whistle, telling ITV: "We talk about being ready. We're a big team at being ready.
"When it matters, you might get five minutes, one minute, but you can make a difference , you can win us a tournament.
"He's been waiting, he's been patient. What he did was outstanding and he deserves it."
Jude Bellingham added: "Ollie Watkins came on and took his opportunity. I'm buzzing for him. You're not starting every game like you would for your club and it's difficult."
