Both sides were seeking their first win of the season with the Blues losing 20-34 to the Hurricanes and the Highlanders going down 17-32 to the Crusaders in last week's opening round.
Williams opened the scoring in the first half and grabbed another in the second half as the Blues scored three tries to two in a match that was keenly contested without rising to great heights.
While Williams starred for the Blues, well-travelled Highlanders first five-eighth Michael Hobbs was himself in a southern hero.
Having scored two tries last week, Hobbs scored another tonight which he then converted to help his side into a 12-7 lead at halftime.
The former Hurricane and Blues player also tackled well and controlled the backline attack.
The Blues, led out by hooker Keven Mealamu in his 97th match for the franchise, got their scoreboard ticking early.
Williams, in his first match of the season, was heavily involved in the try, sparking the move from inside his half.
As the Blues backline smoothly moved the ball upfield, the fullback was on hand for the final pass to cross after breaking a feeble tackle by Highlanders wing James Paterson in the eighth minute.
First five-eighth Stephen Brett nailed the difficult conversion.
But there was no time for the Blues to celebrate as the Highlanders' reply came within minutes.
Paterson atoned for his poor tackle when he featured in a powerful drifting run from midfield and his pass found fullback Israel Dagg who crashed over in the corner.
Hobbs missed the conversion but there was no stopping him in the 24th minute.
The Blues bungled a five-metre defensive lineout and Highlanders halfback Jimmy Cowan grabbed the ball to feed Hobbs who ran over the top of opposite Brett to score.
Hobbs made the conversion from in front of the posts and the Highlanders took a 12-7 lead which they held into halftime.
The Blues' hopes took a blow in the 25th minute when centre Isaia Toeva came off with an injury.
He was replaced by Rene Ranger in a Blues side which did themselves no favours by conceding a number of penalties.
Williams also created his second try which in the 52nd minute put the Blues back into the lead.
His clearing kick was charged down, putting all his players in front of him onside and prop John Afoa thundered upfield, before gifting a supporting Williams the final pass for the converted try.
The Blues took control thereafter through their forwards and Ranger finished off a series of surges which had pinned the Highlanders into desperate defence.
There was no coming back when the Highlanders lost lock Josh Bekhuis to the sinbin late in the game although Dagg had earlier closed the gap with a 59th minute penalty.
Both captains agreed the Blues' two quick tries in the second half were decisive.
"It gave us a little bit of confidence and just a little bit of self-belief and that goes a long way," said Mealamu.
"We know how hard it is to come down to Carisbrook, it's one of the toughest games you get in the Super 14 so we're delighted with the result."
Highlanders captain Jimmy Cowan said his team wanted better before departing for three matches in South Africa.
"We had a great first half, didn't we? ...but a couple of soft tries in the second half really got their vibe going and they put us away in the end."
