Jankauskas has missed the last six weeks due to injury, but looked full of running as he tormented the visitors.
There is no doubt that the crucial point in the game came after just three minutes when Scott McDonald missed a great chance to head Motherwell in front. His header from Richie Foran's cross came back off the post and Hearts broke upfield to score.
Calum Elliot played in Rudi Skacel, and his blistering left-foot shot produced a fine block from Colin Meldrum, but Jankauskas was first to react and slammed home the rebound from six yards.
It took a fine save from Meldrum to push away Skacel's shot, but he was helpless when Hearts went further in front after 14 minutes. Jankauskas found Deividas Cesnauskis down the right and, as Martyn Corrigan cleared his cross, Jankauskas rifled home from 18 yards.
Motherwell were rarely seen as an attacking force, although Jim Hamilton brought a good save from Craig Gordon before the interval.
But Hearts always looked likely to increase the lead, and Cesnauskis and Skacel combined for Elliot to score midway through the second half. The youngster still had plenty to do when he picked up Skacel's flick, but he coolly lobbed home.
Motherwell kept pushing for a consolation goal with both Richie Foran and Steven McGarry missing the target with long-range efforts.
Now Hearts look well positioned to clinch second spot in the league, provided they can keep their off field problems at bay.