For the second straight year, shares of Warren Buffett's Berkshire Hathaway have outperformed the benchmark S&P 500 stock index.

Berkshire's Class A shares finished 2013 at $177,900, just below their 52-week high of $178,900 set in late July. That's up 32.70 percent from their $134,060 close in 2012. It's the biggest annual gain since 1998 when the shares soared 52.2 percent.

Berkshire's Class B shares gained 32.17 percent, closing at $118.56, up from $89.70 at the end of last year.

The S&P had its best year since 1997 with a spectacular gain of 29.60 percent, excluding dividends, but that's just below Berkshire's surge.

In 2012, the stock also came out ahead with a gain of 16.82 percent versus the S&P's 13.41 percent.

By Buffett's favored measurement, however, 2012 was "subpar."

(Read More: Berkshire Hathaway's 15 biggest stock holdings)

In his annual letter to shareholders released in March, Buffett compared Berkshire's per-share book value to the S&P 500 with dividends included. Berkshire's gain of 14.4 percent lagged the S&P's of 16.0 percent.

Buffett was disappointed, writing, "When the partnership I ran took control of Berkshire in 1965, I could never have dreamed that a year in which we had a gain of $24.1 billion would be subpar ... but subpar it was."

We won't know how Berkshire did by the book value metric until the company releases the next letter to shareholders in a few months.

Over the past ten years, Berkshire's stock has gained 111.16 percent, easily outpacing the S&P's 66.23 percent increase.

—By CNBC's Alex Crippen. Follow him on Twitter: @alexcrippen