On the advices of Ankit Sharma and KutuluMike, I'm jotting down my comment here:
Though Thawne could run faster than Barry, he never had the full grasp on speed-force. Eventually, he lost the connection with speed-force just after killing Nora. That's why he had to re-create the particle accelerator explosion to give Barry the speed so that he might help him go back to his time. However, he could charge up himself with tachyon pulse generator; but that's another point.
But the crux is that Thawne could time-travel but for some reasons he lost his connection with speed-force.