Titleholders 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 a thrilling match 5-3 at Young Boys Bern, while fellow Premier League side Newcastle were held to a goalless draw at Maritimo in Funchal.
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 Marseille.
Borussia Moenchengladbach 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.
Napoli striker Vargas, signed from Universidad de Chile in January amid high expectations, scored his first goals since his move.
Vargas latched on to a through ball from Alessandro Gamberini to open his account after six minutes and scored from another pass from the same player at the start of the second half.
Marek Hamsik set up Vargas's third but was given a straight red card shortly afterwards.
Rapid Vienna lost 2-1 to Norway's Rosenborg behind closed doors as a punishment for the crowd trouble which preceded their qualifying tie in PAOK Salonika.
- Eduardo Vargas
- Hapoel Tel Aviv
- Atletico Madrid
- AEL Limassol