The Cats were marginally in front after a solid first quarter but Williamstown stole the lead during the second term and held on to a five-point buffer at half-time.
The contest remained tight during an even third quarter and Geelong continued to trail by five points leading into the final term.
But the Seagulls managed to break away during the last, kicking four goals to the Cats' two, to run away with the 11.14 (80) to 9.12 (66) victory and move up a rung on the VFL ladder to seventh position.
Geelong now sits one game but still plenty of percentage ahead of second-placed Werribee, who defeated the Box Hill Hawks by 34 points on Saturday.
Cats coach Ron Watt said last night he was disappointed his side did not make use of its opportunities in the last quarter.
``We just didn't play well and neither did Williamstown really but they made better use of their opportunities than we did,'' Watt said.
``We didn't play to our capacity and that's disappointing.
``There was only a kick or two in it during the early part of the last quarter but then they kicked a couple away and we just couldn't peg them back.''
Marc Woolnough earned Geelong's best on ground honours for his excellent showing in defence while Will Slade, Daniel Foster and Gary Ablett were other standout performers in the Cats' solid backline.
Peter Street made a welcome return to form in the ruck and also provided a focal point up forward for his teammates.
David Mensch performed well in front of goals for the Cats, contributing two majors, while Matt McCarthy was another dual goalkicker for Geelong.
James Bartel proved useful in his return to the side, chipping in a single goal while Daniel O'Brien, Luke Powell, Will Slade and Street rounded out the goalscorers with a major each.
Watt said he hoped Geelong could resume its winning run when it hosts Essendon at Skilled Stadium this weekend, the second of four consecutive home games for the Cats.
``That was our first loss at home this year, the ground has been pretty good for us so hopefully we can get back on track,'' Watt said.
Geelong plays the Bombers at Skilled Stadium on Sunday from 2pm.