World number 268 Whiteford, from Kirkcaldy, followed a steady opening 71 with a nine-under-par second round of 63 that briefly put him two shots clear of the field at Stockholm's Bro Hof Slott course.
But the afternoon starters found a riposte to his morning heroics, and 20-year-old Italian Manassero surged to the front of the field with a 65, after yesterday's 66, that put him on 13 under par.
Finland's Mikka Ilonen matched Whiteford's 63, and that nudged him one ahead of Whiteford into outright second place, two off Manassero's sizzling pace.
Manassero landed the fourth title of his blossoming career on Sunday when he won the BMW PGA Championship at Wentworth, and there has been no holding him back in Sweden so far.
He reached the turn in a healthy two under par but five birdies on the back nine saw him shoot past Whiteford.
Low scoring was the order of the day, with the temperature warm and the sun out, and Whiteford relished the chance to set an early clubhouse target.
"It's a good start but there's a long way to go. I've had nine under two or three times in my career but I've never gone better than that," he said on the Tour website.
"I have been swinging pretty well over the past month but today was special.
"It was near perfect conditions and the golf course is in great shape."
Whiteford, 32, has never won on the European Tour but he had an impressive second place at the recent Ballantine's Championship in South Korea, where he lost out in a play-off to Australian Brett Rumford but nevertheless collected his biggest career pay cheque of almost £165,000.
He finished off in style today, pitching in for an eagle at the 622-yard par-five 15th which he followed up with birdies all the way home.
Dutchman Joost Luiten reached nine under after a 67.
Swedish players Jonas Blixt and Alexander Noren were flying the flag for the hosts. Blixt signed for a 66 and Noren a 69 as they reached eight-under 136, one ahead of compatriot Rikard Karlberg, Italian Francesco Molinari, Denmark's Thomas Bjorn, and Welshman Jamie Donaldson.
The first-round co-leader, Spaniard Pablo Larrazabal, recovered from a triple-bogey six at the short 11th hole, with four birdies thereafter repairing the damage and giving him a round of 70. It was not ideal, given the conditions, but enough to move him alongside Blixt and Noren on eight under.
With the cut at two under par, England's Paul Casey squeezed through on that mark and so did Australian Andrew Dodt, in extraordinary fashion.
Dodt made two holes-in-one in his round, the first player to achieve that feat on the European Tour, as he went straight from tee to cup on the seventh and 11th holes in a round of 65, after yesterday's 77.
Ireland's Peter Lawrie missed out by a stroke, despite a second round of 67.
England's Simon Khan also had to contend with a weekend off. Last week he tied for second at Wentworth, but rounds of 71 and 73 left him with unwelcome time on his hands.