First, Namikaze Minato can avoid Deidara's bomb tolerance by moving at high speed.
Secondly, Namikaze Minato's Ninjutsu is more harmful to individuals, while Deidara's Ninjutsu is more effective to groups, so Namikaze Minato will have a greater chance of winning one-on-one combat.
Third, Namikaze Minato has chakras in Kyubi no Youko. A lot of chakra can make Namikaze Minato fight for a long time, but not Deidara.