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Ghana international Caleb Ekuban’s 76th-minute header lifted the north-western port side to their first home win this season.
Former AC Milan and Chelsea player Shevchenko took over in early November, replacing Davide Ballardini after a miserable start to the campaign.
It was the Ukraine forward’s first club management role after coaching his national side for five years.
Shevchenko’s Genoa desperately needed a result with their only success in the league back mid-September against fellow strugglers Cagliari.
“I’m really very happy, the squad suffered a lot today and it was important for us to get back winning,” said Shevchenko whose side play Milan in January.
The 45-year-old scored 175 goals in 324 matches in two spells with Milan, twice emerging as Serie A’s top scorer and winning a league title and the 2003 Champions League.
Promoted Salernitana crashed out of the competition as they also sit bottom of Serie A with a seven-match winless run in the league.
Elsewhere, Udinese and Venezia also advanced to the last 16 with wins over Crotone (4-0) and Ternana (3-1) respectively.
