The former Charlton striker took a kick to the leg and was forced off at the Liberty Stadium.
Bolton are easily the lowest scorers in the Championship with just 22 goals from 35 matches.
Magennis has netted four times in the league – also bagging a hat-trick in the FA Cup against Walsall – while veteran Clayton Donaldson has scored once since January 20 2018.
Forward Christian Doidge had to go back to Forest Green Rovers in January after Bolton could not afford to push through a permanent deal for the 26-year-old – he initially came on loan until the start of the new year.
Wanderers have won just two league games since October 24 and look to be paying the price for a lack of investment in their squad – particularly in terms of options in their frontline.
One bright spot has been the form of Remi Matthews, who had been a loan target for Charlton in January. The Norwich City goalkeeper was initially brought in as back-up to Ben Alnwick, out with a back problem, but has done well in an overworked role of late.
David Wheater and Craig Noone were both sent off against the Swans – the latter for two yellow cards – and will serve suspensions.
“Nooney’s sending off is just a terrible decision,” said Bolton boss Phil Parkinson. “It’s a block challenge. I honestly don’t know how you can tackle any fairer than he did. I can’t see how he gave a yellow card for it.
“I have the benefit of seeing them again, and the second sending-off is a sending-off. There are no covering defenders. But the first one wasn’t even a booking.”
Marc Wilson (calf) and Yanic Wildschut (thigh) are sidelined.