Janko scored his 13th goal of the season to sit two ahead of Wellington Phoenix's Nathan Burns in the race for the golden boot.
Having netted nine goals in the last six matches, the Austria captain also equalled the Besart Berisha's league record for scoring in most consecutive games.
Sydney now climbs to second spot for a night at least and is one point behind leader Perth as it remains undefeated on away from home this season.
Newcastle stays in ninth spot still looking for just a second win of the season.
Sydney came into the contest in goal-scoring form, having netted 19 goals in its last six games.
The struggling but improving Jets began with purpose through and on 17 minutes Edson Montano was played into the box after a well-worked move. The Ecuadorian, however, skewed his shot wide from a tight angle.
Sydney FC started to look more dangerous as the first half wore on and was desperately unlucky not to go in front on 29 minutes.
Sebastian Ryall found himself free in the box from a set piece delivery but his header crashed against the crossbar.
From the follow up, in-form striker Janko volleyed the ball goalwards. It hit the arm of Newcastle defender Daniel Mullen and went wide of the upright.
The Jets responded less than five minutes later with Mitch Cooper going on an impressive run through the middle of the pitch before hitting a low shot across the face of goal that flashed passed the Sky Blues post.
Five minutes into the second half it was Sydney FC that again should have taken the lead.
Deep inside his own half, Scott Neville inadvertently played the ball straight to Janko in the area. Despite being one-on-one with Ben Kennedy, the goalkeeper closed the Austrian down quickly enough to block the shot.
Terry Antonis and Janko both had follow-up efforts, yet the Jets managed to scramble away for a corner.
After the hour Newcastle had its own golden chance to open the scoring.
Serbian midfielder Enver Alivodic picked out a free Andrew Hoole in the box, but the Young Socceroos winger headed straight at Vedran Janjetovic.
On 67 minutes Sydney FC finally made the breakthrough.
Substitute Robert Stambolziev stole the ball from Ki Ji-Lee inside the Jets half and played Janko through on goal.
While his first attempt from an acute angle was blocked, the Austrian slotted in the rebound to edge the Sky Blues ahead.
It was the A-League top scorer's 13th goal of the campaign and his sixth straight, equalling the competition record.
Sydney and Janko had further chances to add to the lead, but the solitary strike proved enough to secure the Sky Blues 100th win and second spot on the ladder.
