The former Addicks, Leeds and West Ham midfielder was placed in temporary charge after Karl Robinson’s departure to Oxford United on Thursday.
Lewis Page got Bowyer’s reign off to a flyer with his first senior goal.
It was a cracker from the edge of the area, after just three minutes.
Wolves loanee Michal Zyro added a second to condemn Plymouth to a first defeat in nine matches and give Charlton’s hopes of reaching the play-offs a shot in the arm.
With Blackburn due to the international break not in action, Shrewsbury took advantage with a 1-0 win over AFC Wimbledon taking them back into top spot.
Stefan Payne tucked away a cross from Carlton Morris for his 13th goal of the season shortly after half-time.
Paul Hurst’s side held on for all three points despite a late red card for Bryn Morris.
Wigan Athletic moved up to second thanks to 2-0 win at basement-boys Bury.
Nick Powell converted a Michael Jacobs cross for his 13th of the campaign to give them a 26th-minute lead.
Centre-back Chey Dunkley headed the second just after half-time to keep Paul Cook’s side title hopes well and truly alive.
The Latics visit Fratton Park on Easter Monday and a carnival-like atmosphere is expected.
It will be the first time former Blues boss Cook returns to PO4 since departing for the DW Stadium in June.
Dominic Poleon’s goal gave Bradford their first win under manager Simon Grayson at the fifth attempt of asking.
Poleon struck from 25 yards three minutes into the second half as the Bantams sank Gillingham 1-0 at Valley Parade.
Fleetwood Town’s recent revival continued with a 2-0 victory over struggling Northampton.
Kyle Dempsey’s first goal since last April after 18 minutes set the ball rolling and Cian Bolger wrapped up the three points seven minutes from time.
It was the Cod Army’s first home win since the end of October.
Former Millwall defender Tony Craig netted his first goal for Bristol Rovers but Danny Lloyd levelled four minutes later to secure a 1-1 draw for Peterborough.
Lowly Rochdale were on course for a third straight away win when Callum Camps thumped them ahead from long range but Scunthorpe snatched a point through Ivan Toney’s header.
Later in the evening, the Iron parted company with boss Graham Alexander – despite sitting fifth in the table.
Goals in each half from Stephen McLaughlin and Simon Cox earned Southend a 2-0 win over Rotherham.
Chris Powell’s troops at Roots Hall after just seven minutes.
Cox played a neat ball through to McLaughlin, who stayed composed to give his side the lead with a neat left-footed finish.
Cox turned from making to goalscorer 11 minutes from time when he skipped past Semi Ajayi before firing home to deliver Southend the three points.
Former Pompey striker Michael Smith had a header cleared off the line for the Millers late one.
Finally, relegation-threatened MK Dons drew 0-0 at home to Blackpool.