Melbourne Victory are W-League champions for the second time but they did it the hard way with a last-gasp extra-time winner over Sydney FC in Sunday's grand final.

There were 119 minutes and 58 seconds on the clock at Sydney's Jubilee Stadium when Kyra Cooney-Cross's corner evaded Sydney FC goalkeeper Jada Whyman in a jam-packed penalty area to secure the win.

The pair were the game's key protagonists with teenage midfield prodigy Cooney-Cross behind all of Victory's best attacking moments, while Whyman almost single-handedly kept her side in the contest with a string of saves.

Sydney FC survived an onslaught at times in awkward blustery and cold conditions in front of 4619 spectators, but managed to force the game into an additional 30 minutes.

Player of the match Whyman made an incredible double-block on the goal-line from Cooney-Cross in the second half, and twice athletically pawed away long-range efforts from Annalie Longo.

Matildas' prospect Cooney-Cross and the age-defying 36-year-old Lisa De Vanna both struck the crossbar in the first half and the match seemed set to be the first W-League title decided by penalties before Victory received overdue reward.

"I was just thinking that I didn't want it to go to penalties," 19-year-old Cooney-Cross said.

"We had so many chances, hit the crossbar... kudos to Jada, she made a lot of saves but we deserved to win."

Sydney FC started as mild favourites after seeing off Victory a fortnight ago with a 2-1 win to claim the premiership on the final day of the regular season.

It is a second title win for the Victory following their 2014 success while Sydney FC missed the opportunity to sit alongside Melbourne City with a record-equalling fourth championship.

Victory boss Jeff Hopkins, who became the first coach to claim three W-Leagues titles, said he always felt his team would be victorious.

"Although we were quite confident through the latter half of the game, things were still really tight, they defended really well and were very well organised, so we were living on our nerves a little bit towards the end," Hopkins said.

"I always felt like we were going to get something, even as it came towards the end and had gone to penalties, I felt we would go on and win."

Despite Sydney FC's youthful side, the Sky Blues boasted more grand final experience than their opponents with a cumulative 18 appearances across seven players in the starting side, against 11 appearances from four players for Victory.

Sydney FC coach Ante Juric, who had led the Sky Blues to a fourth-consecutive grand final, said his side missed the pace of the injured Cortnee Vine, and also Princess Ibini in the latter stages after the winger went off injured.

"To concede a goal like that from a corner which wasn't a corner is very disappointing because they (our players) didn't deserve that," Juric said.

"In saying that, Victory were the better team and hat's off to them."