It gave the 29-year-old Irishman a one-shot lead over the Londoner Peter Mitchell and he is two ahead of Domingo Hospital, Jean Van de Velde, Wayne Riley, Eduardo Romero and Tony Johnstone.
"I would have gone to America if I had got an invitation to the Bay Hill," said Clarke. "But when I heard that the Portuguese Open had been switched to Penina I was quite keen to come here.
"This is one of the better courses in Europe and I know it quite well. I first played here nine or 10 years ago when I came over with the Irish amateur team and I lost in a play-off in this tournament here to Adam Hunter three years ago.
"You never like losing a play-off so it would be nice to make up for it with a win here this week."
Clarke does not think his chances in the US Masters will be diminished by missing Bay Hill. "It does not make any difference. It is not the courses you play but how well you are playing that matters."
That said, Clarke's record in America is poor. He has played only three majors in there, missing the cut in the US Open in 1996 and the US PGA championship last year with a best finish of tied 43rd in the 1997 US Open.
And although he equalled the Penina course record with his 66 it will not count because preferred lies were being used as balls were collecting mud in certain damp areas.
Clarke had five birdies and an eagle three at the 478-yard 18th, his ninth hole, where he was on the green with a drive and a five-iron and sank a 10-foot putt. But, unlike most of the field, he played the front nine, easily the most difficult half, in a four-under-par 31 after turning in 35.
Seve Ballesteros, meanwhile, shot a one-under-par 72 and contented himself with a shrug, saying: "It was not too good, not too bad."Reuse content