I want to leave the other switch in place and have the timer work on the other 3 way switch. Is this possible? I've capped one of the two wires, but the timer switch (Leviton) is pulsing on and off?

It is only possible if you tell us the part number of the switch. Leviton make many timers.

It is a No. 616IT. Decora, 500W, Present Electroc Timer Switch, with 10-20-30-60 minute presets. The light slowly pulses from on to off every 2-3 seconds or so. The switch hums. There light says it is a single pole, but I've read where some folks have been successful installing a timer on a light that has 2 switches. Thanks for the help.