The 21-year-old striker netted in the 88th minute of a 3-0 home win against Southend, having replaced Will Grigg in the 64th minute.
And that result took the Latics above Shrewsbury - who Toney spent time on loan with last season.
Elsewhere in League One, Bradford suffered a rare defeat, despite taking the lead against Bury. Alex Gilliead played the whole game. Meanwhile Blackpool drew 1-1 at Walsall, with Sean Longstaff playing the first 63 minutes and picking up a yellow card.
In the Championship, Adam Armstrong started for Bolton Wanderers as they beat Sheffield Wednesday 2-1. It was their first league win of the campaign and Armstrong played for the first hour. Former United winger Sammy Ameobi was on target for the Trotters.
Callum Williams helped Gateshead to qualify for the first round proper of the FA Cup, courtesy of a 2-1 win at Buxton in former Newcastle man Steve Watson's first game in charge of the Heed. Right-back Williams won the penalty which led to Gateshead's first goal before being substituted in the 74th minute.
Stuart Findlay played the whole game as Kilmarnock beat Partick Thistle 2-0 while Matz Sels was an unused substitute for Anderlecht as they beat Mechelen.