Full-back Maicon juggled the ball three times before cracking an unstoppable volley into the corner of the net in the 75th minute.
Eto'o then fired home a mis-hit Sulley Muntari shot in stoppage time to wrap up a victory that will boost Inter's morale ahead of Tuesday's Champions League semi-final first leg against Barcelona.
"It's a very important, hard-fought victory," Inter captain Javier Zanetti told Sky television after his 500th Serie A game. "Now we'll see what Roma do on Sunday.
"On Tuesday we'll face the best team in the world at the moment for their consistency and the players they have. Let's hope we have a good night."
Eto'o and fellow forward Diego Milito wasted chances before Maicon finally broke through with his flash of brilliance.
Substitute Mario Balotelli then hit the crossbar and Eto'o grabbed the second goal in the second minute of stoppage time.
"It's a nasty blow. It's hard to swallow," Juve coach Alberto Zaccheroni said.
"I have to raise morale again for the umpteenth time. We have to conjure up new energy and keep fighting till the end."
