The Moscow court had ruled against any move by Transneft to halt pipeline shipments of Rosneft's oil, Reuters reports with reference to Interfax.
Transneft has not yet agreed a deal with Rosneft for 2017 on transporting its oil and oil products, the company said.
"Rosneft is the only one which has not signed deals on oil and oil product shipments with Transneft," Transneft spokesman Igor Demin said earlier.
Rosneft has also lodged a claim with Moscow's Arbitration court against Transneft, a spokesman for the pipeline company said.
They have also recently locked horns over transportation tariffs related to the new Zapolyarye-Purpe pipeline in northern Russia.