Title holders Atletico Madrid won 3-0 at Hapoel Tel Aviv but Athletic Bilbao, the side they beat in last season's final, struggled to a 1-1 draw at home to Hapoel Kiryat Shmona, another Israeli side.
Among the other matches of the 24 played, Liverpool won 5-3 at Young Boys in an enthralling but blunder-prone tie and Tottenham Hotspur had two goals harshly disallowed in a goalless draw at home to Lazio.
The outstanding individual performances were from Chile striker Eduardo Vargas, who grabbed a hat-trick in Napoli's 4-0 win over AIK Stockholm, and AEL Limassol goalkeeper Matias Degra who extended his remarkable run of not conceding from the penalty spot.
Inter's 2-2 draw means that neither they nor rivals AC Milan have managed a win at the San Siro this season in seven attempts between them.
Inter appeared set for defeat when Venezuelan forward Jose Rondon put the Russians ahead in the 84th minute, however Nagatomo popped up to turn in Diego Milito's cross for the hosts in the second minute of stoppage time.
Rubin had also taken a first-half lead through Aleksandr Ryazantsev with Marko Livaja levelling six minutes before the break.
There were also dramatic finishes at Udinese, where Antonio Di Natale struck in stoppage time to give them a 1-1 draw at home to big-spending Russians Anzhi Makhachkala, and at Fenerbahce, who conceded two late goals in a 2-2 draw with Olympique Marseille.
NINTH MISS
Borussia Monchengladbach should have taken three points from their trip to Cyprus to play AEL Limassol but Oscar Wendt smashed a penalty against the crossbar in the eighth minute of injury time.
According to the Cyprus Mail, it was the ninth time in a row that Limassol's Argentine goalkeeper Degra, who foiled Gladbach earlier with some outstanding saves, had survived a penalty against him.
Liverpool, fielding a reserve team in Switzerland, were gifted a fourth-minute lead with a bizarre own goal when Christoph Spycher headed the ball straight at Juhani Ojala and it ricocheted into the net.
Liverpool returned the present when Enrique lost the ball in the penalty area and Raphael Nuzzolo fired into the roof of the net in the 38th minute.
Liverpool led again and Young Boys turned it around to 3-2 before a Sebastian Coates header, aided by more shambolic defending, and two strikes from Jonjo Shelvey gave the visitors the points, maintaining a 41-year unbeaten record against Swiss opposition.
Clint Dempsey and Steven Caulker both had goals ruled out for Tottenham, who were shunted out of the Champions League qualifiers to make way for holders Chelsea, while Alvaro Gonzalez thumped a shot against the bar for Lazio at White Hart Lane.
Napoli were the only Italian side not to draw as Vargas, signed from Universidad de Chile in January amid high expectations, scored his first goals since his mov
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