The ex-England international grabbed a late winner as Jubilo Iwata claimed a 2-1 victory over Urawa Reds - their first win since gaining promotion.
He tweeted: "I didn't realise I'm the first Englishman to score in the J League since Gary Lineker in 1994."
Lineker scored nine goals in 23 appearances for Nagoya Grampus Eight before announcing his retirement.
He retweeted Bothroyd's post, then replied: "Hope you score more than me. Shouldn't take you long."
Bothroyd, 33, earned his only England cap in September 2010 when he appeared as a second-half substitute in a 2-1 friendly defeat by France. In the process he became Cardiff City's first England international in the club's 111-year history.
He started his career at Coventry City, and has also had spells at Blackburn, Charlton, Wolves, Stoke, Queens Park Rangers and Sheffield Wednesday.
Bothroyd also played for Muanghong United in the Thailand Premier League before moving to Japan in 2015.
Jay Bothroyd has become the first Englishman to score in the Japanese league for more than 20 years.