WENTWORTH, May 23, 2014 (AFP) - Bjorn finished the day with a level par 72, ten shots higher than his opening course record whilst Lowry, the 2012 Portugal Masters winner, shot a 70 with birdies at the last two holes.
The pair are four shots clear of Luke Donald and Spaniard Rafa Cabrera-Bello who were six-under after 36 holes with the Englishman finishing with a flourish by holing from 24-feet for birdie on the last and a round of 67.
Cabrera-Bello was one-over for the day, shedding shots at the 15th and 17th, but stayed in the hunt when he too birdied the 18th.
There are a clutch of big names on the leaderboard with Henrik Stenson and Rory McIlory also making progress on day two.
McIlroy, Paraguay's Fabrizio Zanotti and Swedish pair Jonas Blixt and Stenson were all on 139 - five-under par - and Stenson could become world number one this weekend depending on how Adam Scott fares in America.
Bjorn was never going to match Friday's 62 with tougher pin positions and rain falling when he started his round and he was two-over at the turn.
Birdies at the 12th, 15th and 18th however put him in the hunt for his 16th win on the European Tour.
Bjorn said: "I have got the experience and I know what it takes to win golf tournaments - but I also know that it can quickly disappear over 36 holes.
"A lot of things can change in this tournament from here on in but as long as I stay focussed on my game we'll see where I am on Sunday.
"For a European Tour player this is the biggest event we play outside of majors and World Golf Championships. That says it all."
Donald's round, on a happy hunting ground for him, included nine single putts and got him right back in contention for the European Tour's biggest event which he won in 2011 and 2012.
Donald said: "Being nine behind after the first round it seems like you have got a mountain to climb but now I am only four back and in a position to win this championship again."
McIlroy has been the centre of attention at the European Tour's flagship event after announcing the break-up of his relationship with tennis player Caroline Wozniacki on Wednesday.
He has a poor record on this course - he has missed the last two cuts here - but looked to have buried his demons with his first round until the course hit back on Friday before his final flourish.
And McIlroy has managed to keep the off-field distractions in check as he bids for a first win in the European Tour's flagship event where he missed the cut in the last two years.
McIlroy said: "Three over par after seven holes was not great but it was not disastrous and I knew I would have chances on the back nine.
"There are still 36 holes to go and I feel like I am playing well enough to shoot something in the 60s tomorrow. I am playing well enough to get myself in the mix.
"Once you get inside the ropes you can concentrate on the golf. It is four or five hours of release to get everything out of your head."
Defending champion Matteo Manassero missed the cut after finishing seven-over.
Other casualties included European Ryder Cup captain Paul McGinley, Charl Schwartzel, Ernie Els and Darren Clarke whilst Retief Goosen withdrew after six holes on Friday with back trouble.
Leading and selected scores from the second round of the European PGA Championship at Wentworth on Friday (par 72):
134 - Thomas Bjorn (DEN) 62-72, Shane Lowry (IRE) 64-70
138 - Rafa Cabrera-Bello (ESP) 65-73, Luke Donald (ENG) 71-67
139 - Jonas Blixt (SWE) 68-71, Rory McIlroy (NIR) 68-71, Henrik Stenson (SWE) 68-71, Fabrizio Zanotti (PAR) 67-72
140 - Anders Hansen (DEN) 71-69, Seve Benson (ENG) 71-69, Pablo Larrazabal (ESP) 69-71, Thomas Aiken (RSA) 68-72, Marcel Siem (GER) 69-71
141 - Andy Sullivan (ENG) 70-71, Joost Luiten (NED) 70-71, Chris Doak (SCO) 69-72, Bernd Wiesberger (AUT) 70-71, Ricardo Santos (POR) 72-69
142 - Ian Poulter (ENG) 70-72, Lee Westwood (ENG) 71-71, Jamie Donaldson (WAL) 73-69, Marc Warren (SCO) 73-69, Eddie Pepperell (ENG) 69-73, Mikko Ilonen (FIN) 71-71, Richie Ramsay (SCO) 70-72, Simon Thornton (IRE) 74-68, Gary Stal (FRA) 66-76, Mark Hooper (ENG) 71-71
Selected
143 - Justin Rose (ENG) 70-73, Paul Lawrie (SCO) 72-71, Martin Kaymer (GER) 68-75
144 - Miguel Angel Jimenez (ESP) 72-72
145 - Francesco Molinari (ITA) 71-74, George Coetzee (RSA) 75-70, Eduardo Molinari (ITA) 75-70, Branden Grace (RSA) 70-75, Padraig Harrington (IRE) 69-76, Thongchai Jaidee (THA) 72-73
147 - Masahiro Kawamura (JPN) 73-74, Jeev Mikha Singh (IND) 72-75
148 - David Howell (ENG) 71-77, Jose Maria Olazabal (ESP) 77-71, 149 - Dawie Van Der Walt (RSA), Justin Walters (RSA) 67-81
149 - Shiv Kapur (IND) 70-79, Garth Mulroy (RSA) 71-78, Darren Clarke (NIR) 75-74
150 - Ernie Els (RSA) 72-78, Jbe Kruger (RSA) 75-75
151 - Jin Jeong (KOR) 80-71, Kiradech Aphibarnrat (THA) 73-78, Matteo Manassero (ITA) 80-71
153 - Charl Schwartzel (RSA) 75-78