The 31-year-old slipped walking off the first tee when he resumed the Portugal Masters and feared for a while he might have to withdraw.
But after a physio was called for and strapping applied to his left foot, Fisher battled on and thanks in large part to a 22-foot eagle putt on the long 17th added a 67 to his opening 65.
"I didn't think anything of it at first and for two or three holes it was okay, but then it started to get really sore," he said.
"The physio told me I was not doing any damage by playing on. It was uncomfortable for a while, I was feeling it again at the end and I'm just very relieved to get through.
"To be leading is very, very pleasing. It was really difficult to get through the ball and it made it quite challenging to pick the right club.
"My balance was not very good, but I tried to grind it out and fortunately I came through with a decent score."
On 10 under par at halfway Fisher leads by three from Scot Stephen Gallacher and Austrian Bernd Wiesberger.
Gallacher, yet to have a bogey, is seeking only his second victory in nearly 400 Tour events, but Wiesberger has already had two this season.
Fisher last tasted success at the Irish Open two years ago, a victory which helped to secure him a Ryder Cup debut at Celtic Manor.
Since partnering Padraig Harrington to two wins against the Americans, however, he has managed only one top five finish and finds himself down at 140th in the world.
Gallacher shared the first round lead with Fisher, but had 17 pars and a lone birdie at the 589-yard 17th for a 70 on his return to the Oceanico Victoria course.
Wiesberger shot 65, setting the early target after Harrington had finished disappointingly.
The Dubliner, without a Tour win for over four years, went two clear with six birdies in his first 11 holes, but although two more birdies followed his card also contained a double bogey and two bogeys - both the result of three-putting.
"I'm a little bit upset with them - they hurt a lot more than the double bogey," he said after slipping back into a tie for fourth with Swede Fredrik Andersson Hed on six under.
At least he still has a chance. Ryder Cup hero Martin Kaymer crashed out on two over, although that was still six better than European captain Jose Maria Olazabal on his return to action after the drama of Medinah two weeks ago.
Defending champion Tom Lewis and Scot George Murray, third after his opening 66, made their first cuts in nine starts - but with nothing to spare after rounds of 73 and 76 respectively.
Francesco Molinari, the other member of Olazabal's side in the field, also finished the day on level par.