Stanford's Patrick Rodgers and Georgia Tech's Seth Reeves matched Niebrugge, an Oklahoma State sophomore, at 9-under 135 at The Alotian Club. Rodgers had a 68, and Reeves shot 70.
Niebrugge, from Mequon, Wis., is trying to win for the third straight week after he followed his Public Links victory with a win last week in the Wisconsin State Amateur.
Play was suspended because of darkness after a rain delay.
After the completion of the round, the field will be cut to the low 44 and ties for the final two rounds of stroke play. The final low 16 will advance to match play.