A key point in the game, shortly after the Ravens burned their first timeout, was the challenge play by Harbaugh on the Charlie Batch sack and subsequent incomplete.
This was nowhere near an incomplete pass, and the Ravens coaches up in the box had a clear view that this was not a fumble. In fact, it didn't even look like a fumble when it first happen. Batch was clearly in the process of being sacked, and threw it away near the feet of Isaac Redman at the last possible second.
That challenge cost them their second timeout.
Then injury inside 2 minutes cost them their final one and made things much easier for the offense to control the tempo of the game.