Kevon Smith Snr. was eating at the restaurant in Willoughby, Ohio, when he noticed an older couple in the corner who 'kept smiling' at him and the toddler.
The message he found on his windshield contained money to pay for the meal along with the message, 'Today your meal is on my wife and me'.
The author told him to enjoy spending time with his son, Kevon Smith Jnr., 'as long as God intends.'
The note was later posted on Facebook.
Smith, who teaches basketball, said he was especially moved by the note because he grew up without a father figure.
He told Cleveland 19 : 'There's a lot of guys I know that aren't taking care of their kids,' said Smith.
'To show that not all of us are out here being gang bangers, some of us are out here being fathers.'
Smith joked on Facebook that his son was 'famous at four months' after the generous act, which was widely shared on social media.