Stoltenberg, who took office last month with the crisis top of his agenda, said Russia's continued presence and support for the rebels violated international law, as well as Ukraine's sovereignty and territorial integrity.
Moscow denies that it has any military presence in Ukraine or that it supplies pro-Russian rebels there with weapons.
Kiev and the rebels agreed a ceasefire on September 5, which has been frequently breached.
The accord was subsequently widened to include a military pull-back but many of the provisions remain to be implemented as the death toll in the conflict tops 3,700.
Doing so would "contribute to deescalate the tension and create a more stable framework for a political solution," he said during a visit to SHAPE military headquarters near the west Belgian town of Mons.
Stoltenberg said it was "of great importance" that all sides respect the result of Sunday's elections, a key step for Ukraine to become a stable democracy.
NATO Supreme Commander General Philip Breedlove said Russia continued to have a significant force on the border with Ukraine.
Earlier this month, Russian President Vladimir Putin said some 18,000 troops were being withdrawn from the border area in an apparent gesture ahead of talks with Ukraine and European Union leaders on the crisis.
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