Lewis, a leading member of the temperance movement in Blackburn, helped found Rovers following a meeting with Arthur Constantine.
He was also vice-chairman of the Football Association and Football League and was once considered to be the world's leading referee.
Rovers have promised to keep the grave tended on a regular basis but is grateful to author Peter Lupson, who rediscovered it while compiling research for his book on football club founders.
"What a tribute to the man," said Lupson. "I find it all very emotional.
"He was one of the great citizens of the town and yet all there was to mark his existence was this neglected grave. But now, thanks to the club, they've put it right."
Gwenda Haydock, a Rovers fan who is a great, great, great niece of Lewis, fears the grave may have fallen into ruin had it not been spotted in time.
"Although I'm family I wasn't aware that John Lewis was buried here," she said. "It was only when I did my family tree I realised.
"It could so easily have fallen into disrepair. And that would have been a great shame.
"I'm really happy we didn't go for a new headstone and that we refurbished the old one.
"We thought it was just stone but when it's been cleaned up it's actually white marble!"
