LISBON, October 11, 2013 (AFP) - Still struggling with a virus which hampered him during last week's Seve Trophy, Lynn had shared a seven-way lead overnight and held his advantage with a second straight 65 following four birdies and an eagle.
Playing in the same group, Waring and Otto recorded 14 birdies and one eagle between them to each finish 12 under par.
Waring, playing on a medical exemption after an operation on a serious wrist injury, shot an eight-under par 63 and Otto a 64.
"I am not going to put too much pressure on myself, I've had a medical (exemption) all year so it's nice to get back into a proper category for next year," said Waring, who is currently 86th on the Race to Dubai.
Austria's Bernd Wiesberger completed a 65 to lie one shot off the lead on 11 under alongside Scotland's Chris Doak, who had five birdies and an eagle for 64.
"I'm very pleased," said the 35-year-old Doak, who is 112th on the Race to Dubai with only the top 110 after next week's Perth International keeping their full playing privileges for next season.
South African Justin Walters was a further shot back after at round of 63.
Leading second round scores in the Portugal Masters at the Oceanico Victoria Golf Course, Algarve, Portugal, on Friday (GBR/IRL unless stated, par 71):
130 - Hennie Otto (RSA) 66 64, Paul Waring 67 63, David Lynn 65 65
131 - Bernd Wiesberger (AUT) 66 65, Christopher Doak 67 64
132 - Justin Walters (RSA) 69 63, Alvaro Quiros (ESP) 65 67
133 - Ross Fisher 67 66, Jamie Donaldson 65 68, Matthew Baldwin 67 66
134 - Soren Kjeldsen (DEN) 69 65, Victor Dubuisson (FRA) 67 67, Simon Thornton 65 69
135 - Felipe Aguilar (CHI) 65 70, Paul Lawrie 69 66, Alejandro Canizares (ESP) 67 68, Nicolas Colsaerts (BEL) 68 67, Julien Quesne (FRA) 66 69
136 - Mark Tullo (CHI) 66 70, Maximilian Kieffer (GER) 65 71, David Horsey 67 69, Martin Kaymer (GER) 68 68, Danny Willett 69 67, Jaco Van Zyl (RSA 69 67, Jose Manuel Lara (ESP) 67 69, Pablo Larrazabal (ESP) 69 67, Anthony Wall 68 68, Tommy Fleetwood 67 69, Gonzalo Fdez-Castano (ESP) 69 67
Selected
137 - Thomas Bjorn (DEN) 74 63, Paul McGinley 71 66
138 - Andrew Dodt (AUS) 72 66
139 - Garth Mulroy (RSA) 70 69
140 - Francesco Molinari (ITA) 68 72, Thomas Aiken (RSA) 71 69, Miguel Angel Jimenez (ESP) 71 69, Richard Green (AUS) 71 69
Missed cut
141 - Keith Horne (RSA) 70 71, Park Jun-sub (KOR) 70 71, Brandon Stone
(RSA) 71 71, Shiv Shankar Prasad Chowrasia (IND) 73 69
144 - Thongchai Jaidee (THA) 73 71, Jose-Maria Olazabal (ESP) 72 72
150 - Dawie Van Der Walt (RSA) 79 71