Wong and Lewis both shot a 3-under 69 in the second round on Tuesday to finish 36 holes at 5-under 139, one stroke better than three other players.
The championship was back on track after two weather stoppages on Monday forced the completion of the first round until Tuesday morning. The top 64 players moved on to match play, which begins Wednesday and ends with the 36-hole final on Sunday.
Defending champion Kimberly Kim was among the players who advanced following a long second day at Crooked Stick. After becoming the youngest U.S. Women's Amateur champion ever last year -- she was 14 -- Kim posted two rounds of 73 to keep her hopes of a repeat alive.
No player has repeated since Kelli Kuehne in 1996.
Jennifer Song, So Yeon Ryu and Mi Jung Hur tied for third place behind the co- leaders, coming in at 4-under 140 overall. Like the leaders, Ryu had a 69 in the second round, while Song and Hur posted 73 and 72 respectively.
Song had shared the first-round lead with Candace Schepperle at 5-under 67 after completing her first 18 holes on Tuesday morning. Schepperle fell back with a 79 in the second round, but still made the cut by six shots at plus-2.
The co-medalists, Lewis and Wong, are separated in age by six years.
The 22-year-old Lewis was the individual NCAA Division I champion at Arkansas.
'The medalist hasn't had that much success,' said Lewis, who had five birdies and two bogeys in the second round. 'I was just playing for par and I got the putter rolling.'
The 16-year-old Wong is playing in her fourth U.S. Women's Amateur.
'It was good to have that experience because I knew the field was tough and the courses are always difficult, so staying patient was the main thing,' said Wong, who had four birdies and a bogey.