Moyes admitted his men were fairly good in terms of their standard performance but insists he will take winning in that manner.
The Hammers were tipped to beat the Austrian side by the bookmakers but had to suffer to secure a second win in Group H.
Declan Rice opened the scoring on the 29th minute mark, but Wien were much in the game and had a penalty overturned by VAR on 72 minutes before Said Benrahma sealed the victory in the dying embers.
"OK, pleased we won but we did not play as well as we would have liked. We made a few changes but we are in a lot of competitions and we have to make it work for the whole squad,” Moyes told reporters after the game.
"It was a really good goal and pleased for Declan Rice, he is doing that more, driving forward and getting into the box.
"The minute the referee gave the penalty, I thought it must have been. I was disappointed initially that Ben Johnson had dangled his leg out but when the referee got called over he does not touch him at all. Thankfully it was not given.
Moyes says he hopes the English side win the group and also focus on the Premier League despite admitting it will be very hard.
He added: "I want to try and be in Europe after Christmas by finishing one or two so we want to win the group if we can. We are not going to let up, we are enjoying it and won't be letting it go easy but I have to manage Premier League games too.
"We are capable of handling it and the squad we have can handle it too. It will be tough but I hope we can manage it."
