The Briton qualified on pole with the upgraded engine the champions have brought to the fastest track on the calendar but Rosberg, Hamilton's closest rival 28 points adrift, is using an older one and will start fourth.
The German said after qualifying that the problem would compromise his race.
Mercedes motorsport head Toto Wolff had also expressed some concern about Hamilton's engine while mechanics examined Rosberg's.
However the team said on Sunday that the problem had been traced to "a leak in the cooling system which contaminated the power unit, not a problem with the engine itself."
They said the unit would be inspected again next week to see whether it could be used again in future races.
Hamilton will be chasing his seventh win of the season later on Sunday with Ferrari's Kimi Raikkonen and Sebastian Vettel second and third on the grid at the Italian team's home race.
(Reporting by Alan Baldwin, editing by Amlan Chakraborty)
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