The players have until Nov. 13 to accept or reject the offer, which equals a $15.8 million, one-year deal.
If a player rejects the offer signs with another team, his former team will receive a compensatory pick following the first round of the June draft.
Upton was acquired during general manager A.J. Preller's shopping spree in December. He led the Padres with 26 home runs and had 81 RBIs.
Kennedy was 9-15 with a 4.28 ERA.