Relegation-threatened Boro twice led at the Riverside Stadium, but an 85th-minute equaliser from Man City's returning forward Gabriel Jesus ensured that the points would be shared.
Agnew has praised his players for showing their "fighting spirit", and has also criticised the referee for handing Man City a penalty in the second period, which Sergio Aguero converted for 1-1.
"It was an enjoyable game to watch. We were disappointed to concede at the end, but I think that the effort and bravery was a credit to the players. That was the fighting spirit that we have shown over the past few weeks," Agnew told reporters.
"From where I was I didn't think that it was a penalty and I thought Sane went down very very easily. I find it strange that the referee can give the penalty from where he is positioned.
"To take the lead twice against a top team is something that is to the credit to my side. There are still nine points to play for and with the spirit that the team has shown, there is no reason that we can't win more matches."
Middlesbrough remain 19th in the Premier League table - six points behind 17th-placed Hull City - ahead of their trip to league leaders Chelsea on May 8.