I have a 2001 Chevrolet Malibu LS and would like to program two key fobs for my car. Does anyone know how?

First you plug your scan tool into vehicle diagnostic connector.........

sorry I don't think you can do this without a scan tool

cant you just ground the two connectors like you would to get the check engine code?

One of my previous vehicles was a 1990 Olds Cutlass Supreme Intl (I really, really liked that car). I bought it used & I only recieved one key fob -- so I had to order another one. On that particular car, there was a wire in the trunk (it was velcro'd to the "roof" of the trunk, kinda where the speakers were at). The end of the wire was tapped off. If you removed the wire & grounded it, you'd hear the door locks activate. You then had to do something goofy like hold down the key fob for 5 seconds & it would tell the car to "learn" that new key fob. That was pretty much it. I'd guess that things have changed significantly from a 1990 model year car to today..

Yes, that is the way GM vehicles used to handle programming. Most have transitioned now to using scan tool.

Same thing with grounding terminals in diagnostic connector to get codes from engine controller through flashing telltale - that was something that went away close to 10 years ago (around the time of original OBD).