The 27-year-old took to the field with a headband at Old Trafford on Saturday to protect a head injury that saw him miss England's FIFA World Cup qualifiers against Moldova and Ukraine.
But he was not hampered, as he curled home a 25-yard free-kick in the 81st-minute to add to Robin van Persie's penalty before half-time.
That gave Moyes a comfortable first home league win, and the Scot was quick to single out Rooney's contribution.
"I thought we played well but I thought we needed to score a few more goals with the build-up play we managed," he told BT Sport.
"He (Rooney) tired a bit in the second half but I thought he was great in everything that he did.
"I wanted him to get 90 minutes under his belt, which is important with the busy week we have coming up."
