The Australian striker, who joined the Lions from Middlesbrough in the summer transfer window, netted the only goal of The Valley clash in the 38th minute to open his account for the south Londoners.
McDonald's deflected shot allowed Millwall to record their second straight win, lifting them to 17th on the Championship table, and delighting manager Steve Lomas in the process.
"I'm pleased for Scott," said Lomas.
"We probably ask him to play slightly out of position on the left but it worked a treat today. He got a bit of luck with the deflection but he earned it.
"It's the first Sunday in a while I'll have a coffee and read the papers."