His rushed par-save attempt ended up further past the hole than his original birdie attempt, with McIlroy requiring another two putts - taking his tally to four from inside six feet - to eventually nudge in a double-bogey six.
Monterey Peninsula is a par-71, while Spyglass and the host Pebble Beach courses are par-72 layouts. "I just felt like I played really solid, hit a lot of really good shots, hit a lot of good putts and it was a pretty easy day".
Johnson has made a fine start to this year, winning the Tournament of Champions before a top-10 finish at the Abu Dhabi HSBC Championship.
Rory McIlroy says he is comfortable with his current game. "It's probably the first time, too, I think we have ever played over there with nice weather". It is the first tournament of the calendar year for Scott, who used a conventional putter having tried his old long putter at the Australian PGA Championship late last year.
The Monterey Peninsula has been a good hunting ground for Johnson with two wins (2009 & 2010) and a runner-up (2013) finish as well as a third place past year.
Health department offering free flu shots in Hampton
So far, influenza A/H3 viruses have been most common this season, however, influenza A/H1 and influenza B are also circulating. Whatever the reason, "it's a whopper of a flu season", said Mimi Dreifuss, a North Carolina nurse who got sick this week.
"But with how I was sort of dejected and wanting to get away from it I was then, to how rejuvenated and optimistic I am now, it feels a lot different that way".
Ahead of this week's Pebble Beach Pro-Am, the Australian said four-time Major victor McIlroy possesses all the tools to dominate the sport in a manner similar to Tiger Woods in the late 1990s and early 2000s but raised doubt over 'how much he wants it'. That put him alongside Mickelson in the group of six players sharing fifth place on nine-under, which also included former world number one Jason Day who posted a six-under 65 at Monterey Peninsula.
Rory McIlroy and Jon Rahm are just three adrift of the lead at four under.
McIlroy was four-under through 15 holes before suffering a bogey on the 16th, when his wayward drive finished in a waste area.
He almost drove the green and putted his eagle attempt to within 10 feet.