All eyes will now be on the other group match between Poland and Colombia - defeat for either side will be the end of their tournament in Russian Federation.
Sadio Mane gave Senegal the lead in the 11th minute, deflecting the ball into the net for his first World Cup goal, but Takashi Inui equalized with a well-placed shot from inside the area in the 34th.
Senegal boss Aliou Cisse chose to put three up front for the match at Ekaterinburg Arena, his team's first against an Asian opponent at a World Cup.
But the statistic most of Japan will want to remember is that Honda ended a 15-international game scoring drought that began in September 2016.
"Despite that we were leading twice and what is annoying were the two goals (conceded)". "We didn't lose today".
While he is known for his quiet outward demeanor, the man of the match in Japan's win over the 10-man Colombians in Saransk has a powerful presence within the Samurai Blue squad, according to his teammates.
For Sadio Mane, it was a wasted opportunity. "I have confidence. Our team has the quality to face Colombia", he added, looking forward to Thursday's meeting with the South Americans in Samara.
Nigeria vs. Iceland live stream
They must avoid defeat against Argentina on Tuesday if they are to stand any chance of reaching the knockout stages. The Super Eagles take on Iceland on Friday, June 22 at the Volgograd Stadium Kick off 4PM Nigerian time.
Mane, fresh off the back of an exciting club season that took Liverpool to the Champions League final, felt the Africans deserved to win.
"But after that I think we did pretty well".
"The best team on the pitch was Japan, we have to admit", said Cisse, who as captain led Senegal to the quarter-finals in 2002.
However, Takashi Inui equalised for Akira Nishino's charges in the 33rd minute with curling low strike that found the bottom corner.
Veteran Honda, 32, who became the first Japanese player to score in three different World Cups, replaced Shinji Kagawa in the second half with his team down 2-1 and fired the equaliser in 12 minutes from time after an error by Senegal goalkeeper Khadim N'Diaye. Keisuke Honda has been involved in six of Japan's last eight goals scored at World Cups (three goals and three assists), and is now registered at +292 to score a goal anytime in this game.
Salif Sane of Senegal wins a header over Keisuke Honda and Yuya Osako of Japan.
"It is very important to neutralise Mane but we did a pretty good job in dulling his threat, but what we were more anxious about was the impact he has on other Senegal players".