The London team rose up to third place with their 4-0 home win over Rotherham, with Joe Aribo, Lyle Taylor and Krystian Bielik all on the scoresheet at The Valley.
Pompey finished fourth after the 1-1 draw against Accrington, while Sunderland’s defeat to Southend confirmed them in fifth place.
Doncaster made sure of their play-off place with a 2-0 win over Coventry.
It means Charlton face Doncaster away on Sunday, May 12 and then host them on Friday, May 17.
Bowyer is confident the power of his squad will have all the play-off opposition feeling the heat.
They have won three games in a row, scoring 10 goals and conceding none he feels that momentum can be important.
The Charlton boss told News Shopper: ‘It's a good thing to have because, us as a team, the best habit to have is winning games.
‘I know that any of the teams in the play-offs wouldn’t have wanted to play us because we have everything – we work hard, we compete, we move the ball and we create a lot of chances.
‘For me, we’re in a good place. We’ve got a full squad and it’s come at the right time because, when we’ve had a full squad, we don’t lose many games.’
Doncaster beat Coventry with headed goals in each half from Kieran Sadlier and John Marquis.
Peterborough missed out on the play-offs even though they beat Burton 3-1. They finished in seventh place – just a point behind Rovers.
Ivan Toney scored twice for Peterborough.
Meanwhile, Stephen Humphrys’ late goal on Saturday saw Southend beat Sunderland to retain their League One status.
The Shrimpers looked to be heading down before Humphrys struck with just three minutes left to seal a 2-1 win.
John White had put the home side in front at Roots Hall from a corner just before half-time, but Chris Maguire equalised with a penalty in the 75th minute.
Southend’s late show sent Plymouth down, despite the Pilgrims beating fellow relegation batters Scunthorpe 3-2.
At Home Park, it had looked as if Plymouth were going to pull off the great escape as Lloyd Jones and Freddie Ladapo put the home side seemingly in control.
Kyle Wootton pulled a goal back before the break and Josh Morris equalised on the hour, after Pilgrims keeper Matt Macey had tried to throw the ball out to get treatment.
Graham Carey restored Argyle's lead, but events on the Essex coast took fate out of their hands, with relegation confirmed on goal difference.
Walsall’s goalless draw at Shrewsbury was not enough to prevent them from dropping into League Two.
AFC Wimbledon, though, survived after a 0-0 draw away to bottom club Bradford.
Luton made sure of the title ahead of Barnsley, who lost 2-1 at Bristol Rovers.
The Hatters had already secured promotion, and two goals from George Moncur helped see of Oxford at Kenilworth Road.
Elliot Lee was also on target for the home side early in the second half, while defender Luke Garbutt had pulled a goal back for the U's on the hour before Moncur wrapped up the title.
Joe Jacobson scored direct from a corner to give Wycombe a 1-0 win over Fleetwood, which saw the Chairboys pull clear of the survival battle.
Tom Eaves scored twice in the first half as managerless Gillingham won 3-0 at Blackpool.