As milestone-man Adam Scott led a disappointing Australian challenge, Clark cashed in on surprisingly easier afternoon conditions to surge to six under through 16 holes before play was suspended under darkness.
A two-hour fog delay kept the field waiting on Thursday before Scott ground out a three-over-par 73, in his 100th consecutive major championship.
The former world No.1 found himself nine shots off the pace after Clark burst from the pack with an eagle and two birdies in a brilliant back-nine stretch.
The 2023 winner will return early on Friday (Saturday AEST) looking to retain the first-round lead and potentially break the four-under first-round record at the famed layout on New York's Long Island.
Fellow Americans Sam Stevens, Max McGreevy and talented amateur Ryder Cowan all posted two-under 68s in the morning, before gusting winds subsided somewhat to allow Clark's blitz.
Only three players out of 654 have ever finished an Open at Shinnecock under par, and officials are expected to toughen up the layout over the remaining three days.
Already Clark will take some catching.
Another former winner, ex-world No.1 Dustin Johnson, was level pegging with Clark at four under before making a horror three-putt double bogey right before the horn sounded to mark the end of the day's play.
Two more former US Open champions, Jon Rahm and Matt Fitzpatrick, were also at two under late in their rounds as golf's cream rose to the top.
Earlier, play was suspended for two hours after just 30 minutes of action as the fog encircling the course worsened to such an extent that players on the 12th tee in particular could not even see the landing area on the fairway.
Scott wobbled with a double-bogey six at the 16th hole but struck straight back with a birdie on 17 to post the lowest round among the five Australians.
Min Woo Lee was three over through 14 holes when play was stopped.
Lucas Herbert carded a four-over 74 and his LIV Golf Ripper GC captain Cameron Smith a 75.
Smith's round was blighted by a dreaded triple-bogey six at the par-3 seventh hole, when the former British Open champion needed two shots from a bunker and then three-putted.
Former world No.1 Jason Day's 14th Open tilt lasted only nine holes before he withdrew with a back injury.
A grimacing Day bogeyed seven holes to turn in 42 before the 2011 runner-up called for officials and was carted back to the clubhouse for treatment.
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