Kaymer, a favorite for European Tour Rookie of the Year, tied Chapchai Nirat and Lee Westwood for the lowest round this season. Nirat shot his 61 in the first round of the TCL Classic and went on to victory, while Westwood fired his 61 in round one of the Mercedes-Benz Championship, but tied for sixth.
The German Kaymer also established a new course record at Oceanico Victoria Club de Golfe. He won twice last year on the Challenge Tour and has a tie for third and a tie for second on the European Tour in 2007.
'I really enjoyed the day,' said Kaymer, who shot a 13-under 59 last year on a third-level tour in Europe. 'I was playing awesome today. Every putt went in. It was a perfect golf day.'
Martin Erlandsson and Daniel Vancsik, last week's 54-hole leader at the Madrid Open, are tied for second place after opening rounds of 8-under-par 64.
Westwood, two-time U.S. Open winner Retief Goosen and Gregory Bourdy are knotted in fourth place at minus-7.
These five players carded great scores on Thursday, but were not close to Kaymer.
He parred his first two, then rattled off back-to-back birdies from the third. Kaymer posted two in a row again on his front nine, from the sixth, and made the turn in 32.
It was on the back nine that Kaymer got into the record books.
The German birdied the 10th and 12th holes to reach 6 under par for the championship. Kaymer then caught fire at the end of his round to not just take the lead, but tie the European Tour record for the year.
He birdied four holes in a row from the 13th, but needed a birdie at the last to match the low score of the year. Kaymer drained a 15-foot birdie putt at the closing hole to do just that.
'It was a day that everything goes in,' said Kaymer. 'I've been waiting for this day for a couple of weeks. My putting has been so-so, but every putt went in this time.'
Kaymer has enjoyed a spectacular rookie season on tour. He held the 54-hole lead at the Wales Open, but only managed a 1-over 70 in the final round and tied for 14th. At the Scandinavian Masters in August, Kaymer owned first heading to the final hole, but made double-bogey on the 72nd to share second.
'I was in a really good position in Sweden,' acknowledged Kaymer. 'I learned a lot of things. We'll see how it ends this weekend. I'm not thinking about victories. There's still 54 holes left.'
Fredrik Andersson Hed, Ariel Canete, Emanuele Canonica, Alfred Dunhill Links Champion Nick Dougherty, Jean-Francois Lucquin, Andrew McLardy, Francesco Molinari, Alvaro Quiros, Charl Schwartzel, Sam Walker and Steve Webster share seventh place at 6-under 66.
With the season winding down, the Order of Merit title is still up for grabs. Ernie Els and Padraig Harrington are not here this week, but No. 3 Justin Rose is in the field.
Rose, battling a recurring back injury, shot a 3-under 69 on Thursday and is tied for 44th place with, among others, Andres Romero, who is seventh in the money race.