Itachi would win such battle if he's in full power and healthy condition. His advantage is his Sharingan and Mangekyo Sharingan. Although Jiraiya can go into Sage Mode, he's still inferior to Sharingan users. Even Madara wouldn't want to go up against Itachi (since he was only able to fulfill his plans after Itachi's death). Plus, let's compare their statistics:
ITACHI
Ninjutsu - 5
Taijutsu - 4.5
Genjutsu - 5
Intelligence - 5
Strength - 3.5
Speed - 5
Stamina - 2.5
Hand Seals - 5
Total - 35.5
JIRAIYA
Ninjutsu - 5
Taijutsu - 4.5
Genjutsu - 3
Intelligence - 4.5
Strength - 4.5
Speed - 4.5
Stamina - 5
Hand Seals - 4.5
Total - 35.5
For the three main types of jutsus (Ninjutsu, Taijutsu, Genjutsu), Itachi is already superior to Jiraiya. Jiraiya's Senjutsu needs time to be activated, considering the fact that Itachi's speed is a perfect 5, Jiraiya will have a hard time activating it. And besides, it was Zetsu himself who said that when Itachi is using Susano'o, he is completely invincible.
We have already seen Jiraiya at his full strength when battling Pain, and he still lost. On the other hand, Itachi was only shown in partial strength (when up against Kakashi in Part I) or in a dying state when he battled Sasuke, and still Sasuke was unable to defeat him.
Makes sense?