The Latics dropped to 18th in the table and were outplayed by a high-flying Preston side who are now unbeaten in 10 league games.
North End led after six minutes as Chris Humphrey showed superb control before angling in a shot from 14 yards.
Oldham enjoyed a spell of pressure, but Preston doubled their lead in the 71st minute when Humphrey set up Joe Garner for a tap-in.
Gary Harkins pulled one back after 75 minutes with a fine shot into the top corner, but Johnson's side soon went down to 10 men as substitute Jonson Clarke-Harris was shown a straight red card for handling Garner's header on the goalline.
Garner's resulting penalty was brilliantly saved by Mark Oxley, but he bagged his second goal two minutes from time with a dipping 20-yard drive.
Johnson admitted: "It's fair to say we were outclassed.
"Credit where it's due because Preston are a really good side, but it's frustrating that we've started poorly in some of our recent home games.
"We had a go after half-time, but it's easy to play when you're behind because the opposition give you more room.
"You have to be brave and take the game on at 0-0, but not enough of our players did that.
"You can't be shrinking violets. This is an important time in players' careers and they need to stand up and be counted.
"There were times when I looked at some of them and saw worrying traits. Our confidence looked low, even on basic things like pass and control.
"You need to have a good day when you're facing a top side, but too many started with performances that were four or five out of 10.
"Preston fully deserved to win, but we are very disappointed."