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."
Juve, in sixth position, had midfielder Momo Sissoko sent off for a second caution in the 37th minute as defeat represented another blow to their hopes of finishing fourth to qualify for the Champions League preliminaries.
CRISP STRIKE
Juve, who beat Inter 2-1 in December, made a bright start and captain Alessandro Del Piero had a crisp strike from outside the box well saved in the second minute.
Inter gradually improved as tempers rose, with a raft of bookings and fouls before Sissoko was dismissed for hacking down Zanetti.
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."
There were several empty areas in the San Siro as officials tried to avert trouble between the rival fans.
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