The German scored his first goal for the club to put his side ahead in the first half at the Tottenham Hotspur stadium but Erik Lamela scored late on to take the game to a shootout.
Werner had been expected to take a spot-kick but the former RB Leipzig forward was suffering from cramp in the final minutes.
Lampard asked Werner if he wanted to take a penalty but the German declined the offer, fearing he could worsen his pain.
‘We spoke to the players,’ said Lampard afterwards.
‘You work on penalties and try and have a plan but it’s very difficult to know.
‘Timo had some cramp at the end and Timo would have probably taken one so we had to adjust around that.’
It’s likely that Werner would have taken the spot of either Mount or Emerson Palmieri, who was at fault for Lamela’s equaliser.
Tottenham must wait until Thursday to find out their opponents for the quarter-finals.