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."
Moyes will now hope that his men can build on their strong start to the new campaign, in which they have lost just once, when they face Bayer Leverkusen in the UEFA Champions League group stages on Tuesday.
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