After late victories against Huddersfield Town and Southampton, Silva scored with seven minutes on the clock for a City side who, in cantering to an eight-point lead, are showing all the hallmarks of champions-elect.
Meanwhile, Shakhtar Donetsk have reached the knockout stages in three of their last six Champions League campaigns, their best performance dating back to 2010/11 (quarter-finalists).
The 34-year-old Ivorian midfielder has played less of a front-line role this season as young guns Raheem Sterling, Leroy Sane and Gabriel Jesus have helped fire City to the top of the Premier and Champions League tables.
United sealed progression to the competition's last 16 for the first time in four seasons after goals from Romelu Lukaku and Marcus Rashford cancelled out Alan Dzagoev's opener.
"(Marouane) Fellaini a chance, Zlatan (Ibrahimovic) a big chance and (Nemanja) Matic is injured but will play for sure. We will be doing our job here and if we do it well, if we play our best football, that match will not matter.
Manchester City's third successive late victory "shows what we are", manager Pep Guardiola said after David Silva's 83rd-minute winner saw his side equal a Premier League-record 13th successive triumph.
But by the time of their most recent meeting, at the Etihad Stadium in April, thoughts of an all-Manchester title shootout had vanished.
John Stones and Benjamin Mendy are both injured but youngsters Phil Foden, Brahim Diaz, Tosin Adarabioyo and goalkeeper Danny Grimshaw have been included.
"The pace was better, we had more presence in the box". They have a big issue but in the end everybody is ready to play.
City will already be without John Stones for their trip to Old Trafford, with the England international sidelined with a hamstring problem he hopes to return from in time for the Christmas period.
Guardiola was asked for further clarification on the nature of the injury but was unwilling to elaborate.
"He felt uncomfortable after his goal [against West Ham]".
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