I just bought a Programmable timer without realizing that it is labeled as single pole. The switch that I want to replace is three way. The other switch on the circuit is located in the garage and never used. Can I use the single pole switch or do I need to get a three way switch?

Yes, conditionally. The condition being that the other 3-way switch is never used.

Connect the wire that was on the common of the 3-way switch you removed and one of the other wires that was connected to the switch, to the timer switch. Cap the remaining wire with a wire nut.

If the timer switch does not work, flip the switch in the garage to the other setting.

Another approch would be to connect the wire on the common to the timer. Connect the other two wires together and add a pig tail. Connect the pig tail to the timer switch. That would make the switch in the garage ineffective. Won't hurt anything if some one changes the switch in the garage just to see what happens.