All three judges scored it 120-108 for the 30-year-old Williams, who improved to 41-2 with 27 KOs.
"It feels really good. Ishida's a good fighter but we put in good work," Williams said. "We're going to make it back to the top of the game."
Ishida, a 36-year-old from Japan, dropped to 24-7-2 with 9 KOs. He had recorded a stunning, first-round knockout of WBC Continental Americas light middleweight champion James Kirkland last April.
Williams entered the bout hoping to redefine the direction of his suddenly stuttering career after being knocked out in the second round by Sergio Martinez in a WBC middleweight title fight 16 months ago and winning a controversial 12-round majority decision over lightly-regarded Erislandy Lara last July.
“We’re in a much-needed position where we need to have Paul come back and show his greatness,” Williams’ trainer George Peterson said about the Ishida bout earlier in the week. “Every great champion has gone through this and this is where we are.”