Moore had a 9-under 207 total on the Crosswater Golf Club at Sunriver Resort. Wake Forest's Kyle Reifers (73) was second, followed by Oklahoma State's Pablo Martin (71) at 7 under and Texas A&M's Andrew Parr (69) at 6 under.
Moore, coming off consecutive victories in the Perry Maxwell Invitational in Ardmore, Okla., and the NCAA Central Regional in Cleveland, had five birdies and a double bogey Friday.
Washington shot a 6-over 294 on Friday for a 7-under 857 total, with the top four scores each day from the five-player squad counting in the total.
'It was tough out there,' Washington coach Matt Thurmond said. 'We shot 6 over and I thought we played pretty well. Our round was 12 shots different than yesterday's round, but I felt like the guys really hung in there, played hard and finished well.
'Nobody likes the rain. Nobody likes to carry an umbrella and rain gloves, drying stuff off all day. It's a grind all day. It's tough, but this is the national championship. So you just find a way to enjoy it and make the most of it.'
Oklahoma State shot an even-par 288 in the third round to match Wake Forest and Arizona State at 4-under 860. Minnesota and Lamar were tied for fifth at 1 over.
'I'm glad the conditions were like they were today, because I don't think we would have done very well if this would have turned into a birdie-fest,' Oklahoma State coach Mike McGraw said. 'We got some weather today and handled it well. We were able to take advantage of it and put together one of the day's better rounds.'
Washington had three players in the top 12 in the individual standings. Zach Bixler (73) and defending champion James Lepp (71) were tied for fifth at 5 under, and Alex Prugh (74) was tied for 12th at 3 under.
'I hate playing in rain like this,' Lepp said. 'So, I'm very pleased with a 71. Hopefully, tomorrow we'll get some normal golf weather and it will lead to better things.'