Yes. Savings bonds cashed for education qualify for the interest exclusion. Depositing money into a 529 plan counts as "used for higher education". After entering the 1099-INT (with an amount in box 3), the Turbotax (TT) interview will ask "Did you use the U S Savings Bonds to pay higher education expenses?". Answer yes.

The next screen will verify that your particular bonds qualify. Then you will be asked details about the amounts, your student-beneficiary and the name of the Educational Institution (in your case the 529 plan)

There are AGI limits for doing this. (https://www.treasurydirect.gov/indiv/planning/plan_education.htm)