The Cameroon striker, as lively as his bright yellow boots, has been outstanding this term and took his season's tally to 11 goals in all competitions, while also helping set up Wesley Sneijder for the other goal.
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So often forced to play wide and sacrifice himself for the team last season under Jose Mourinho, Eto'o has been thriving again, while strike partner Diego Milito has struggled following his heroics during last term's treble.
"I'm happy to win now as an attacker having played last year as a defender," Eto'o joked to reporters, having earlier celebrated his third by taking a picture with a pitchside photographer's camera.
Esteban Cambiasso won a challenge in midfield and Eto'o took a heavy touch with his knee before prodding the ball between Tim Wiese's legs for the 21st minute opener.
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He then seized upon extraordinarily lax Werder defending to finish off Lucio's ball over the top before playing provider for Sneijder to smash in the third after 34 minutes.
Eto'o got to keep the ball as a memento once he rounded the goalkeeper to score nine minutes from time after a lifeless second half, which started with a chastened Werder being sent on to the pitch minutes before Inter appeared.
'ALWAYS DANGEROUS'
"Last year Samuel played as a striker sometimes but often out wide but this year I've moved him closer to goal and when he is near goal he is always dangerous," coach Rafael Benitez told a news conference after his first home European game at Inter.
Injuries to Milito and Goran Pandev meant Eto'o could finally make the most of leading the line against Werder from the start, alongside youngsters Coutinho and Jonathan Biabiany.
Mumbles spread across the San Siro when fans witnessed the inexperienced teamsheet, also missing captain Javier Zanetti and centre back Walter Samuel as in Saturday's defeat at AS Roma.
The noises turned to groans as the European champions, who drew 2-2 at Twente Enschede in their opener, made a poor start with Werder's Hugo Almeida lobbing the onrushing Julio Cesar only for Lucio to clear before missing another good chance.
The Inter faithful need not have worried, though, and they were soon waving their giant flags in delight after injury-hit Werder's defence caved in.
"I don't know if it was their birthday today but we gave them too many presents," said Werder coach Thomas Schaaf, who was so angry he made his side warm down on the pitch at the end.
The only negatives for Serie A leaders Inter were injuries to Julio Cesar and Lucio ahead of Sunday's game with Juventus.
"It's not a good sign when two players have to leave the field but it doesn't seem too serious. We'll wait for tomorrow," Benitez added.
Inter top Group A after two games and next host Tottenham Hotspur, who drew 2-2 at Werder in their opener but beat Twente 4-1 on Wednesday.
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