Maguire, 24, and Chalobah, 22, have both been selected in an England squad for the first time.
Chalobah moved from Chelsea to Watford in July, while Maguire joined Leicester from Hull City in a £17m deal in June.
Uncapped Everton goalkeeper Jordan Pickford is also in the squad.
England, who have a two-point lead in Group F with four qualifying matches left, face Malta, bottom of the group, on 1 September and Slovakia at Wembley three days later.
Manager Gareth Southgate confirmed that he had considered recalling Everton striker Wayne Rooney before the 31-year-old, who has scored a record 53 goals for the England team, announced his retirement from international football on Wednesday.
"I called him, but he said he had been thinking long and hard about his decision and he announced his international retirement," said Southgate.
"I was thinking of including him in the squad. His form has been excellent. If you are the most capped outfield player and record goalscorer, I am not sure what else you have to do to be an England legend.
"He has served his country brilliantly and I congratulate him on a fantastic international career."
Southgate said he had been impressed with Maguire for a long time.
"I thought his performances for Hull were very good," said Southgate.
"He is a defender who is very comfortable with the ball, he has already adjusted very well to a new club at Leicester, plays with composure and can defend the ball into the box, so this is a good chance to have a look at him.
"Chalobah and Pickford were both excellent at the Under-21 European Championships and deserve the opportunities."
Middlesbrough defender Ben Gibson and Southampton goalkeeper Fraser Forster, who were in the squad for the 2-2 draw with Scotland and the 3-2 friendly defeat by France in June, have not been included in the 28-man squad.
Liverpool midfielder Adam Lallana has not played this season because of a thigh injury, while Tottenham left-back Danny Rose is recovering from a long-term knee injury, and Manchester United full-back Luke Shaw is only just returning to fitness after four months out with ankle ligament damage.
England's first squad of the post-Wayne Rooney era sees two of the younger brigade rewarded for fine early-season form.
Nathaniel Chalobah's bold decision to leave Chelsea in search of regular football sees him in Gareth Southgate's squad while central defender Harry Maguire's fine start at Leicester City earns him inclusion.
It may yet be one of the squad's elder statesmen who makes the headlines. Joe Hart's long-held status as England's first-choice keeper is threatened by his own decline in form and the increasing quality of Stoke City's Jack Butland and Everton's young summer signing Jordan Pickford.
Hart was exposed badly once more by two Leigh Griffiths free-kicks in the 2-2 draw with Scotland at Hampden Park in June's World Cup qualifier, and it may well be that Southgate decides the time is right for change, with Butland likely to get first crack at making the number one spot his own. On current form, Hart is third among those keepers chosen.
England would hope for relatively comfortable rides in these two qualifiers to take further strides towards the 2018 World Cup in Russia but places are up for grabs in all areas so there may be even more motivation for those picked by Southgate.
England squad to face Malta and Slovakia
Goalkeepers
Jack Butland (Stoke City), Joe Hart (West Ham United, on loan from Manchester City), Tom Heaton (Burnley), Jordan Pickford (Everton).
Defenders
Ryan Bertrand (Southampton), Gary Cahill (Chelsea), Aaron Cresswell (West Ham United), Phil Jones (Manchester United), Michael Keane (Everton), Harry Maguire (Leicester City), Chris Smalling (Manchester United), John Stones (Manchester City), Kieran Trippier (Tottenham Hotspur), Kyle Walker (Manchester City).
Midfielders
Dele Alli (Tottenham Hotspur), Nathaniel Chalobah (Watford), Eric Dier (Tottenham Hotspur), Jordan Henderson (Liverpool), Jesse Lingard (Manchester United), Jake Livermore (West Bromwich Albion), Alex Oxlade-Chamberlain (Arsenal), Raheem Sterling (Manchester City).
Forwards
Jermain Defoe (AFC Bournemouth), Harry Kane (Tottenham Hotspur), Marcus Rashford (Manchester United), Daniel Sturridge (Liverpool), Jamie Vardy (Leicester City), Danny Welbeck (Arsenal).
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