The Mariners edged their F3 derby rivals thanks to Patricio Perez's last-minute strike to grab their 16th win of the season and take their unbeaten run to nine matches.
Arnold said it was a solid performance and reflected on his side's regular season achievements.
"I thought overall it was a very good performance," said Arnold.
"The patience and discipline we showed in the second half was very pleasing. In the past we would have gone too gung-ho in search of a result.
"Newcastle made things difficult for us by putting players behind the ball, but in the end we had seven or eight good chances to their one, and we took it well so I think we deservedly won the game.
"We spoke before the game that we haven't kept a clean sheet for a while. Our focus has been on a strong defensive structure and today it was very good. The conditions weren't easy tonight, a lot of rain and strong wind meant there were some loose touches and passes, but overall I think we played well.
"At the start of the season we set ourselves the goal of conceding one goal a game. We missed out on one but to score 50 in a season, and concede only 31, I'm very proud of their efforts."
The second-placed Mariners will now prepare for the first leg of their two-legged semi-final clash with Premier's Plate winners Brisbane Roar which kicks off at Bluetongue Stadium on Saturday night.