ST ANDREWS, October 3, 2014 (AFP) - Jacquelin shot a 70 at the pro-am event to move nine under par -- one shot ahead of Irish duo Shane Lowry and Padraig Harrington, England's Oliver Wilson and France's Alexander Levy.
Eleven of the top 12 scores came from players who were at Kingsbarns on Friday and Carnoustie on Thursday, when calm conditions meant traditionally the hardest of the three venues played relatively easy.
Wind and rain made scoring more difficult on Friday but Jacquelin birdied his final two holes to move into pole position for a fifth European Tour title.
"I'm pretty happy, especially the way I finished. I birdied 17 and 18 so it was good before having dinner and going to rest," Jacquelin said.
"I've been working hard every year since the last 20 years to be at this position. I feel good. It's a long weekend."
Lowry, who finished joint third in this event 12 months ago, was the only player in the top 12 to play at St Andrews on Friday, meaning he will face Carnoustie on Saturday before the final round is again played over the Old Course.
"To be honest, the way I played to shoot two under was quite good," said Lowry after a round containing four bogeys and six birdies.
"The forecast was pretty bad today and everyone was expecting the worst, but it wasn't actually that bad."
Scottish duo Richie Ramsay and Chris Doak are two shots off the pace on seven under, with compatriot Stephen Gallacher another shot back and Gallacher's European Ryder Cup team-mate Rory McIlroy five off the lead on four under.
McIlroy started the day nine shots off the pace and dropped back to two over par with a bogey on the 14th.
However, the world number one responded in style with a superb fairway-wood approach to the par five 16th and rolled in the eagle putt from 15 feet on his way to a round of 67 at Kingsbarns.
"I think the eagle on 16 kickstarted something for me," he said. "I just went from there, started to knock a few putts in.
"I felt like I struck the ball pretty well for the first couple of days, but just to see a few putts roll in sort of gave me a little bit of confidence and played well after that."
Leading second round scores in the European Tour's Alfred Dunhill Links Championship at St Andrews, Carnoustie and Kingsbarns on Friday (GBR/IRL unless stated, par 72):
Kingsbarns
135 - Raphael Jacquelin (FRA) 65 70
136 - Oliver Wilson 64 72, Padraig Harrington 66 70, Alexander Levy (FRA) 68 68
137 - Richie Ramsay 69 68, Ryan Palmer (USA) 69 68, Christopher Doak 70 67
138 - Felipe Aguilar (CHI) 71 67, Stephen Gallacher 68 70, Gregory Bourdy (FRA)
67 71, George Coetzee (RSA) 71 67
139 - Richard Sterne (RSA) 73 66
140 - Victor Dubuisson (FRA) 71 69, Robert Karlsson (SWE) 72 68, Rory McIlroy 73 67, Soren Hansen (DEN) 72 68, Mark Foster 68 72
141 - Thorbjorn Olesen (DEN) 71 70, Branden Grace (RSA) 76 65, Edoardo Molinari (ITA) 73 68
St Andrews
136 - Shane Lowry 66 70
139 - Hennie Otto (RSA) 69 70, Jamie McLeary 67 72, Brandon Stone (RSA) 72 67, Richard Green (AUS) 68 71
140 - Matthew Nixon 70 70
141 - Thomas Aiken (RSA) 71 70, Thriston Lawrence (RSA) 68 73, Paul Lawrie 69 72, Ryan Evans 67 74, Nick Dougherty 72 69, Garrick Porteous 74 67, Ashley Hall (AUS) 71 70
142 - Lucas Bjerregaard (DEN) 74 68, Richard Bland 71 71, Richard Finch 72 70, Justin Walters (RSA) 69 73, Scott Jamieson 70 72
143 - Robert Jan Derksen (NED) 73 70, Paul Waring 71 72, Peter Lawrie 70 73, Anthony Wall 73 70, David Drysdale 71 72, Romain Wattel (FRA) 72 71, Niclas Fasth (SWE) 72 71, Eduardo De La Riva (ESP) 67 76, Nacho Elvira (ESP) 71 72, Trevor Fisher Jnr (RSA) 70 73
144 - Magnus A Carlsson (SWE) 74 70, Tom Lewis 71 73, Jens Dantorp (SWE) 72 72, Gary Stal (FRA) 69 75
Carnoustie
139 - Ricardo Gonzalez (ARG) 69 70, Chris Wood 70 69
140 - Marcel Siem (GER) 69 71, Graeme Storm 68 72
141 - John Parry 68 73, Andrew Sullivan 70 71
142 - Shiv Kapur (IND) 70 72, Maximilian Kieffer (GER) 72 70, Adrian Otaegui (ESP) 67 75, Michael Hoey 72 70, James Morrison 72 70
143 - Marco Crespi (ITA) 73 70, Robert Rock 67 76, Marc Warren 73 70, Nick Cullen (AUS) 73 70, Oliver Fisher 74 69
144 - Jason Scrivener (AUS) 72 72, Merrick Bremner (RSA) 73 71, Ulrich Van Den Berg (RSA) 71 73, David McKenzie (AUS) 70 74, Anders Hansen (DEN) 75 69, Fabrizio Zanotti (PAR) 73 71, Simon Dyson 73 71, Pablo Larrazabal (ESP) 71 73
145 - Darren Fichardt (RSA) 73 72, Gregory Havret (FRA) 74 71, Julien Quesne (FRA) 72 73