Sweden's Pettersson had five bogeys, two double bogeys and five birdies in a second round of 4-over-par 76, while England's Gilford shot a 72.
After 80 players finished the delayed second round Saturday, organizers waited 3 hours before deciding to call off play for the day and reduce the event to three rounds.
'We have three holes -- the 11th, the 15th and the 16th -- that are unplayable,' tournament director Mikael Eriksson said.
Balls were being blown off tees and rolling on the green at the par-3 11th hole.
Only five players broke par through 36 holes. The cut at 9-over was a season high on the European tour.
Miguel Martin of Spain (second-round 70), Greg Owen of England (71), and Henrik Nystrom of Sweden (71) were tied for third place, one stroke back.
When play was abandoned Friday because of the weather, Pettersson held a five-stroke lead and had played three shots on the par-4 7th hole. When action resumed Saturday, the Swede double-bogeyed the hole.
He dropped five shots in his first five holes Saturday, including a double bogey at the 11th.
'The wind was howling there,' Pettersson said. 'A pretty good drive, but it went through the green. And the first chip was impossible.'
Gilford had four birdies and four bogeys.
'I'm delighted,' Gilford said. 'It's very tight and playing long with no run on the fairways. And I could hardly stand up in the wind on the 11th tee.'
Full-field scores from the Algarve Open de Portugal