Freddy Eastwood's early opener for the Shrimpers was cancelled out by Gulls midfielder Joss Labadie on the stroke of half-time
And Knill felt his team could have picked up a vital three points.
"It was an excellent battling performance but if I'm honest I'm disappointed it wasn't three points," said Knill.
"We had the opportunities here but on the whole the performance was as good as I've had since I've been in charge here.
"The players are so committed and we looked a threat and as long as we have got that it gives us a great chance to stay up.
"Southend are in my opinion one of the best teams in the league and no one gave us any hope to get a result here.
"But we created as many chances as them and looked as dangerous as well."
