With the scores level at one goal apiece, Lancaster came off the bench in the 81st minute at Leichhardt Oval and scored a minute into added time to nab the three points for the visitors.
Tuesday night's result was a sucker punch for Sydney FC, who had ended a five-game goal drought through Amelia Cassar's 18th-minute opener.
Their lead didn't last long, with Newcastle winger Melina Ayres' 29th-minute shot going in off the post.
Lancaster's injury-time effort keeps the Jets' unlikely finals hopes alive, with the visitors surging to seventh (4-1-5).
Only goal difference ranks them below sixth-placed Brisbane Roar, who are also on 13 points but have played two fewer games than Newcastle.
While the Jets snapped a four-game losing streak, coach Stephen Hoyle will be without regular centre-back Claudia Cicco against league leaders Melbourne City on Friday.
Cicco must serve a one-game suspension after earning her fifth yellow card of the season for fouling Hana Lowry in the 86th minute.
Sydney FC - five-time champions and premiers - languish in 10th (2-4-4) after extending their winless streak to six games.
Ante Juric's side have now lost their past three games to Newcastle, last winning on January 21, 2024.
A quick-thinking Cassidy Davis had denied the hosts the opener in the seventh minute, with the Jets skipper clearing Skye Halmarick's header off the line.
It was Newcastle winger Josie Allan - on return to the starting line-up - who opened the door for Sydney, giving up possession to Cassar in the hosts' attacking half.
With Newcastle goalkeeper Anna Leat scrambling to return to her line, Cassar ran down the right wing unchallenged and launched from well outside the box to score in spectacular fashion.
The visitors hit back thanks to a cross from Lauren Allen.
Jets striker Haley Johnson's header fell short, but Ayres managed to thread the ball past three Sydney FC defenders to level the scores.
Johnson tried her luck again with a close-range shot just before halftime, but was denied by an outstretched Sky Blues goalkeeper Heather Hinz.
Showing her quality in the second half, Hinz produced back-to-back saves in the 61st minute to deny Ayres and Josie Allan.
Newcastle were lucky to avoid giving away a penalty when Sydney winger Riley Tanner was taken down in the box by India Breier in the 82nd minute.
But Breier was only shown the yellow card after being adjudged to have fouled Tanner just outside the penalty area.
Matildas hopeful Lowry was unable to take advantage of the free kick and sent it over the crossbar.
Sydney midfielder Bianca Galic was left lamenting a missed opportunity when her shot in the 87th minute went just wide of the goal.
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