It was a second successive away defeat without scoring a goal for the Pilgrims and leaves them 21st in the table, just one position and a point clear of the relegation zone.
If Argyle beat Hull City, who need to win to have any chance of making it into the play-offs, at Home Park next Saturday they will be safe and can start preparing for another Championship campaign, but a draw or defeat against the Tigers will open the door for 22nd-placed Birmingham City to move above them and send the Pilgrims back into League One.
Birmingham are at home to fifth-placed Norwich City, who have not yet mathematically secured a playoff place, at St Andrews.
Argyle dropped to 21st after their defeat by Millwall, following an 84th minute headed goal from Jake Cooper, with Sheffield Wednesday climbing to 20th as they beat West Bromwich Albion 3-0 at Hillsborough.
Ben Waine replaced Ryan Hardie in the Pilgrims’ starting line-up against Millwall as one of three changes from the 3-0 defeat away to Steven Schumacher’s Stoke City in their previous match.
The New Zealand international striker got his opportunity after Hardie had gone 10 games without adding to his tally of 13 goals in all competitions this season.
Defenders Lewis Gibson and Ashley Phillips were also brought into the team, as Hardie, Julio Pleguezuelo and Adam Forshaw all dropped down to the substitutes’ bench.
Forshaw was fit to be selected, despite being taken off in the early stages against Stoke due to a tight hamstring, but there was no place in the matchday squad for Jordan Houghton, who had replaced him in central midfield at the bet365 Stadium, due to illness.
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