The 25-year-old American, who has missed the cut in all six of his previous starts on the U.S. circuit, fired an eight-under-par 63 at Monterey Peninsula Country Club, one of three venues being used for this week's event.
Loupe, who tied for sixth at the Web.com Tour's season-ending Tour Championship to earn his card for the 2013-14 PGA Tour, birdied five of his last nine holes on the easiest of three courses to soar to the top of the leaderboard.
"I just keep telling myself, you're supposed to be here, you're going to play good, just keep playing," Loupe told reporters after his flawless eight-birdie display.
"And this is just one round, guys, you know, but I feel good."
Australian Stuart Appleby, who carded a six-birdie 65 on the Shore Course at Monterey Peninsula, was one of five players knotted at six-under before play was suspended for the day in fading light.
Level with Appleby were compatriot Scott Gardiner, who also started out at Monterey Peninsula, and Americans Jimmy Walker, Jim Renner and Richard H. Lee.
FedExCup points leader Walker returned a 66 on the hosting Pebble Beach Golf Links while Renner and Lee both shot 65s on the Shore Course.
Tournament favourite and four-times winner Phil Mickelson was at five-under, having made three birdies and he had just eagled the par-five sixth at Monterey Peninsula, his 15th hole of the day, when play ended for the day.
Mickelson and 39 other players will resume their rounds at 7:45 a.m. Pacific Time (1545 GMT) on Friday before the second round is scheduled to start just over an hour later.
Among the other big names playing this week, three-times major winner Padraig Harrington of Ireland opened at Pebble Beach with a level 72, a score matched by defending champion Brandt Snedeker at Spyglass Hill.
Northern Ireland's Graeme McDowell, who clinched the 2010 U.S. Open staged at Pebble Beach, carded a 71 while Fiji's former world number one Vijay Singh struggled to a 78 at Pebble Beach.
Thursday's opening round was certain to spill over into Friday after heavy rain on the picturesque Monterey Peninsula forced play to be suspended for just under three hours earlier in the day.
With puddles of water forming on many of the greens and bunkers at Spyglass Hill, the action was halted after just 39 minutes of play before resuming at 11:30 a.m. PT (1930 GMT).
Because of the forecast for poor weather, officials had already implemented 'lift, clean and place' for the players during the first round.
Conditions on Friday are expected to be better with just a 20 percent chance of showers but more rain has been forecast for both Saturday and Sunday.
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- Monterey Peninsula
- Pebble Beach