Maarten Lafeber, one of three overnight co-leaders, carded a 2-under 70 to move into second place at 7-under-par 137.
Lee Westwood, the 1999 and 2000 champion here, posted his second straight 69 to take third place at 6-under-par 138. Nick O'Hern, another overnight co-leader, managed an even-par 72 to remain at minus-5.
Goosen, who also won the 2001 U.S. Open, started his second round on the back nine, and opened with a birdie at the 10th. The South African birdied the par-3 13th for the second straight day.
He came right back to birdie No. 14 to get to minus-6. The 35-year-old made it three in row with a birdie at the 15th, then ran off five straight pars around the turn.
Goosen dropped in an 8-foot birdie try at the par-5 third and got to minus-9 with a 12-foot birdie putt at the par-4 sixth.
He parred his final three holes to close out a bogey-free round and maintain his two-stroke cushion on the South Course at The K Club.
'Obviously when you win your first major a lot is expected of you, but when you win your second, people expect even more,' said Goosen. 'I am expecting myself to play well, obviously, I am here to try and play well and see if I can win the tournament. I have a two-shot lead at the moment going into the weekend and it is always nice to be ahead. But it is going to be a long weekend.'
Lafeber opened on the front nine and started with six consecutive pars. He then birdied the par-5 seventh for the second straight round. After two more pars, the 2003 Dutch Open winner birdied No. 10 for the second time in two days.
The 29-year-old wrapped bogeys at the 13th and 15th around a birdie on 14. Lafeber parred the 16th and 17th, before collecting one final birdie at the closing hole to get within two shots of Goosen.
'I actually played better than the score suggests,' Lafeber said. 'I didn't make any mistakes for the first 12 holes and hit 17 greens in regulation. Overall I said that par was pretty good so you can imagine I am very happy.'
James Kingston carded a 4-under 68 to get to 4-under-par 140 where he stands alone in fifth place. Niclas Fasth, David Howell, Jose Manuel Lara, Paul McGinley and the final overnight co-leader, Paul Broadhurst, are one stroke further back at minus-3.
Phillip Price, the defending champion, notched an even-par round of 72. He stands at 3-over-par 147 where he shares 39th place.
The cut line fell at 5-over-par 149 with 78 players advancing to the weekend. Among those missing the cut were Michael Campbell (150), Soren and Anders Hansen, both 151, and Colin Montgomerie (154).