Can I use a centrifuge instead of vacuum when using the QIAquick 96 PCR Purification Kit?

Yes, you can use a QIAGEN Centrifuge with the QIAquick 96 PCR Purification Kit. Follow the Supplementary Protocol 'Spin procedure for purifying 2 x 96 PCR samples using the Plate Rotor 2 x 96, a special centrifuge, and the QIAquick 96 PCR Purification Kit.' Here's the link to the protocol.