The co-leaders shot a 7-under 64 over the TPC Deere Run course, which yielded 90 sub-par scores in the opening round.
The 64 equaled Villegas' low round of the year. His once-promising career has faded over the past two seasons and he missed the cut in six of his first 10 appearances in 2013.
Villegas has shown recent signs of a comeback, however, by making the cut in six straight events. He tied for 10th last month in Memphis.
Johnson and Villegas had a one-shot lead over Brandon de Jonge, Matt Bettencourt and Daniel Summerhays. Recent PGA Tour winner Boo Weekley was among those tied for sixth at 66 while three-time John Deere champion Steve Stricker, Davis Love III and Nick Watney were part of the group at 67.
In addition to moving into contention for a fourth title at this event, Stricker said Thursday he would skip next week's British Open to be with his wife as they celebrate their 20th wedding anniversary.
Jonas Blixt, who won last week at the Greenbrier Classic, struggled to a 74.