To expand upon sivu's answer, this is a common use for so-called "bus switches" which are basically logic-controlled MOSFETs. Using discrete MOSFETs has some drawbacks (parasitic capacitance / capacitive coupling being one) and it can be tricky to choose a good MOSFET. The bus switches are optimized for use in high-speed logic circuits.
Several manufacturers make them, including Fairchild, TI, IDT, and Pericom. Take a look at the NC7SZ384.
Many Arduino's have onboard support to run at 3.3 V. Actually, all can run at 3.3 V and the FTDI chip schematic explains how in an example. Paul, who made the Teensy USB Arduino, had suggested that I could splice the USB cable open and supply a 3.3 V voltage in place of the VCC line of the cable. You could try this. But there are also other options.
Check the logic levels for the Arduino. I believe they support 3.3 V as logic HIGH even on a 5 V sourced Atmel. A SparkFun article states: "*Connecting a 3.3 V digital output pin to a 5 V input pin is often straightforward. Most devices are fairly tolerant to the minimum voltage that they will accept as a digital high value. Most Atmel microcontrollers, for example, accept anything above 0.6*VCC as high, so the 3.3 V device must output a level above 3 V (0.6*5 V).*"
Purchase one of the Arduino clones that has jumpered 3.3 V and 5 V selectors. I use the RBBB cloan which I have set the supply cables FTDI chip to 3.3 V. But there are many others that have actual 3.3 V configuration options, including one of the recent official Arduinos if I remember correctly. You could also use the Teensy USB with his Arduino plugin and follow the directions on his site to install a 3.3 V regulator.
Splice the USB cable and provide a laboratory power supply quality 3.3 V source in place of the VCC line of the USB cable. It should be low current, as Paul has suggested. Hence, either a good quality voltage source. You could also just put a couple of batteries in series to get the desired voltage.
If you are interested, I can try to examine the schematic of your Arduino and perhaps it is possible to make a change to the FTDI configuration that would allow for 3.3 V.