Phaneuf will not play against Los Angeles on Wednesday and at St. Louis on Thursday. He loses more than $66,000 in salary.
During Toronto's loss to Boston on Sunday night at Air Canada Centre, Miller's back was turned at the time. No boarding penalty was called. Miller left the game but coach Claude Julien said he wasn't worried about the defenseman's condition.
Phaneuf had a phone hearing Tuesday with NHL vice president of player safety Brendan Shanahan.
The suspension is the Leafs' fourth this season. The others were to David Clarkson, Nazem Kadri and Carter Ashton.