The average dollar invested in an actively managed equity mutual fund over the past one, three and five years outperformed its benchmark index through June 30, according to a new report released by Standard & Poor’s on Thursday.

The so-called Midyear 2009 S&P Indices Versus Active Funds Scorecard, or SPIVA, compared the returns of active funds vs. S&P benchmarks in a variety of different asset classes. The data takes into account survivorship bias, which eliminates funds that go under or merge into other funds.

Historically, the results of the SPIVA analyses heavily favor the indexes. That’s what happened with the last report, covering year-end 2008, when indexes won in a landslide.

But the Midyear 2009 report contains a surprise. While the average actively managed funds trailed their benchmarks on an equal-weighted basis, when measured on an asset-weighted basis, the active funds won.

For instance, as the table below shows, nearly 63% of all actively managed large-cap funds trailed the S&P 500 over the past five years. But the average dollar invested in those large cap funds actually beat the index by 0.21%. That’s all the more impressive considering that the indexes do not have any expenses associated with them, while the active funds are measured post expenses.

The same or similar results carry through multiple subasset classes on the domestic equity side, such as the growth and value subsegments of the various capitalization benchmarks.

On the international equity side, however, the results were more mixed. For the global category, the active funds won in a cakewalk: The average dollar invested in a global fund outperformed the S&P Global 1200 by 2.07% per year over the past five years. But the indexes won for international funds and emerging market funds.

Full details are available from S&P here.

Interestingly, the story is almost perfectly reversed in the bond space. For fixed-income, the average dollar invested in an actively managed bond fund trailed its benchmark on a one,- three- and five-year basis in every domestic bond category. For global and emerging market debt, the active funds outperformed on a five-year basis, although they still lagged on a one-year and three-year basis.

There is no single explanation in the S&P report for why actively managed funds had this turn of good fortune. In the year-end 2008 report, active funds trailed the indexes on both an equal- and asset-weighted basis in virtually every category. Somehow, the six-month shift has pushed the results in favor of the active funds. It may have to do with strong performance over the first six months of 2009, or it could be attributable to the new starting point of the study (the last six months of 2004).

Either way, the data suggest that investors are putting more money to work in the better-performing actively managed funds, and those funds are doing OK.