After twice going behind, Takashi Inui and Keisuke Honda scored to level the score in the Group H fixture at Yekaterinburg's Central Stadium.
Sadio Mane broke the deadlock in the 11th minute when goalkeeper Eiji Kawashima's save ricocheted off the Liverpool striker into the net before Moussa Wague struck a far post effort to put the Teranga Lions 2-1 up on 71 minutes.
"It was a tough match and we knew it would be tough," Nishino said.
"We came back from behind twice and we knew Senegal were not a team that we could beat easily.
"We pressed well though, and didn’t let them play their way.
"We didn’t let them capitalise on their physicality.
"Towards the end, our players knew how to deal with them and were even running better."
Currently tied on points with Senegal at the top of the table, Japan, who handed Colombia a 2-1 defeat in their tournament opener, need just a point from Thursday's clash with Poland to confirm their place in the last 16.
"Of course, it is very important to neutralise Mane and [Hiroki] Sakai did a pretty good job neutralising him and dulling his threat," Nishino continued.
"What we were more concerned about was him giving a positive impact to other players, especially in the first half when we let him and other players play too freely.
"But after that I think we did pretty well."
The Samurai Blue are hoping to reach the knockout stage of the World Cup for the third time after round of 16 berths in 2002 and 2010.
They made their tournament debut in 1998.