After a rough few years, Jordan Nobbs said she was happy to take her chance with her goal.
The new Women's Super League record of 13 wins in a row was broken by the Gunners.
Goals from Stina Blackstenius and Frida Maanum sealed the victory after Nobbs came off the bench to score.
Nobbs missed the World Cup due to injuries and the Lionesses' triumph at the European Championships due to injury.
Nobbs has had to bide her time for minutes in the middle of the field, but she now has two goals in four days after her strike against the Swiss team.
Nobbs said that everyone on the bench has been working hard.
The mentality is a credit to it. We've had a lot of games, but we know when to play.
I've had a lot of injuries. In the last few months, I've had to work hard because we have such a good squad. I'm happy I was able to take it.
In the end, it was a deserved win for the team and they keep pace with the leaders.
The Hammers should have been two goals up before Nobbs scored the first for the visitors.
The goal that was wrongly ruled out after Kim Little appeared to slip was the one that Nobbs was able to cancel out.
The referee made a decision to penalize her when Little slipped in the box, but she wasn't happy about it.
She poked it over the line from close range after the ball bounced off the post and into her path.
It was the end of the record run of 10 consecutive WSL matches without a conceded goal by the Gunners.
The manager told Sky Sports that they were sloppy with mistakes.
We were able to fight our way back in and win. Quality was added by the three replacements.
Little was taken to the hospital after twisting her knee and was replaced by Nobbs.
Blackstenius volleyed in Catley's superb free-kick in the second half, before Maanum scored her third goal in as many WSL starts when she headed in the ball.
Jordan Nobbs is in the squad.
There is a player that has prepared well. The difference is that she came on with good quality.
Nobbs knows he needs to play to get into the England squad. Sarina made that clear. When I can, I have to take risks. I need to be playing a sport.
Though they are in second place on goal difference, the fact that they have played a game extra means they are level on points with Manchester United andChelsea.
Paul Konchesky, who took over this summer, has three wins to his name from the first six matches of the season.
Last season, they missed out on the WSL title by a point to Chelsea, but they have shown their worth this season.
Six changes were made to the starting XI for Thursday's victory in the Women's European Championship.
Nobbs did not let Little's injury affect his performance.
She picked up her second player-of-the-match award in a row after scoring on Thursday.
When she came on, she forced late saves from the young West ham goalkeeper, making her debut.
Hillyerd was an impressive performer for West Ham as she kept out Blackstenius and Foord, before Maanum struck the post.
In the end, the game was decided by a double save by the goalkeeper and a late strike by the full-back.
West Ham's three defeats this season have all come against the top three teams in the league.
They have a player in terrific form who has scored four goals in six WSL games.
Konchesky said that "we started very well again and for 70 minutes were great but maybe the strength in the squad shows."
It wasn't to be, but we could have had another goal. The person was not happy. You can either get those decisions or you can not. It could have cost us at the end if we hadn't gotten it.