Janzen was one of more than 800 golfers from around the United States who were playing for spots at this year's tournament, which begins on June 13 at Merion Golf Club outside of Philadelphia.
Janzen, the 1993 and 1998 champion, will not be making the trip after he was notified that he violated a club rule by wearing the spikes at his sectional in Rockville, Maryland.
Professionals are allowed to wear metal spikes, but are subjected to club rules during sectionals.
Fellow Major champions Mike Weir and Ben Curtis will also be absent after the duo were unable to make enough progress at their separate sectionals.
Elsewhere around the country, tour winners Charley Hoffman and Bae Sang-Moon advanced in their Columbus, Ohio sectional with Hoffman grabbing top honours over the field.
Jordan Spieth, who has made his mark on tour with a string of strong showings, shared top honours at the Dallas site to also qualify for the Open.
The 19-year-old finished as the top amateur, grabbing a share of 21st, at last year's tournament.
Tour winner Scott Stallings, along with young South Korean talent Noh Seung-Yul, missed out on qualifying.