Salesforce Q3 Beats Expectations: $788M Revenue, 33 Cents Non-GAAP EPS this afternoon posted its financial results for the third quarter of 2012, and the enterprise cloud computing giant’s report bested Wall Street estimates at both the top and bottom lines.

Salesforce reported Q3 revenue of $788 million, up 35 percent year-over year and up 7.6 percent from the second quarter of 2012. On a non-GAAP basis, which is where Wall Street analysts typically evaluate the company’s earnings, Salesforce’s earnings per share (EPS) was 33 cents, a one cent decline from its EPS in Q3 2011 and nine cents down from its Q2 2012 EPS.

Wall Street analysts had expected the company to post revenues of $776.6 million and non-GAAP EPS of 32 cents, according to FactSet, so today’s results surpassed both of those estimates.

According to Salesforce’s CEO Marc Benioff, the company’s recent performance has been strong — compared both with its own history and the sales numbers of its peers. The executive said in a press release accompanying the earnings statement:

“ is the first enterprise cloud computing company to exceed a $3 billion annual revenue run rate, with outstanding third quarter revenue growth at 35% in dollars and 37% in constant currency.”

On a GAAP basis, however, Salesforce’s operations were in the red during the third quarter — GAAP net loss per share was -$1.55. This was due in large part to a $149 million one-time, non-cash income tax related charge incurred during the quarter, the company said. Salesforce’s non-GAAP results exclude that charge as well as certain interest and stock-based compensation expenses.

In all, Salesforce expects to finish the year on a strong note. The company today raised its guidance for revenue and non-GAAP EPS: Salesforce now says its full-year revenue should be between $3.041 billion to $3.046 billion, and its full-year non-GAAP EPS should be between $1.50 and $1.52.