Kaymer tightened his grip at the top of the leaderboard in the PGA Tour's flagship event adding a 69 to his opening course record equalling 63 to move to 12-under par in the $US10m event.
The Dusseldorf-born golfer is looking for a first victory since the pair tasted success in the 2012 Nedbank Challenge at Sun City - a win that came just two months after his bagman gave Kaymer 'the line' to hole the triumphant putt in the Ryder Cup at Medinah.
Connelly was by Kaymer's side when he went to No. 1 in the world in capturing the 2010 PGA Championship at Whistling Straits before hooking up with England's Paul Casey.
The pair have since been reunited following Kaymer's brief dalliance with Christian Donald, the brother of Luke, as his caddie and he appears a happier man for it.
"I didn't realise how good Craig was for me until I arranged for him to again caddy for me two years ago at Wentworth," said Kaymer. "Too often you get caught up in that mindset of being so serious out here with everyone so focused on doing their own thing and so much into themselves.
"With Craig back on the bag we've had a fun time. It's very important you have someone you get along with, both on and off the golf course, as you can sometimes be travelling with them three or four weeks in a row, and like Craig and I are doing over these coming weeks.
"Craig hadn't changed in the time we were apart and I don't think he ever will. I had Christian on the bag for about 13 months but that didn't work out but, with Craig, I really enjoy working with him."
While Kaymer attempts to secure the $1.8m first prize, Jamie Donaldson a potential Ryder Cup team-mate continues to enhance his claim for a place in the team to the face the United States at Gleneagles in September. Donaldson is second on the European Points List and has sought the counsel of Paul McGinley, the captain of Europe, about the progress he ios making.
"I spoke to Paul earlier this week and he was very good with his encouragement he gave me and he told me keep up the good work," said Donaldson. "That's what I am trying to do every week. I'm in a good position at the moment but then there is so much more to achieve before I can even think about qualifying for Gleneagles. So I also need to focus on that and not get excited about possibly playing in my first Ryder Cup."
Donaldson, runner-up in March's WGC-Cadillac Championship in suburban Miami, capped his round with four straight birdies from the ninth hole. The double European Tour winner then birdied 16 and 17 but made a mess of the last in missing a four-footer for par.
There was less encouraging news for the Scottish duo of Russell Knox and Martin Laird who look set to miss the one-under par cut with the former posting a pair of 72s on his debut while the latter, runner-up at Sawgrass two years ago, was heading home early after scores of 76 and 70.
Stephen Gallacher, and the third Scot in the field, was the very last out on day two teeing off at 2.21pm local time (7.21pm UK time).