Both goals arrived in a first half that was almost completely one-sided, as the visitors struggled to deal with the Blues’ attacking play.
Hawkins was the beneficiary of some good work from the hosts’ wide players, as he converted crosses from first Matty Kennedy and then Jamal Lowe.
It was no surprise that the Dons were better after the break, but they did not do enough to test Luke McGee.
Kenny Jackett made one change from the side that won at Gillingham the previous week.
Christian Burgess had recovered from a calf injury to start in defence and make his 100th appearance for the club, allowing Hawkins to move to a more natural position up front.
A slight niggle ensured that Curtis Main was the man to miss out, with Stuart O’Keefe continuing to wear the captain’s armband in Brett Pitman’s absence.
The visitors had an early chance when Osman Sow got past Matt Clarke, only for the centre-back to recover well and win the ball back.
But after that it was a first half that saw Pompey enjoy almost total dominance, as they poured forward at every opportunity.
Kyle Bennett burst free down the right and Kennedy just got a touch to his cross to take the ball away from the advancing Lowe.
But the deadlock was broken on 14 minutes – and Kennedy had a large part to play in giving the hosts the lead.
He intercepted a sloppy pass from Ethan Ebanks-Landell and burst past the Dons defender before teeing-up HAWKINS for a powerful finish into the roof of the net.
There was a scare for both teams when Kennedy and Callum Brittain disappeared over the advertising hoardings at the Fratton End.
But the Blues winger soon reappeared and, after some treatment, the visiting right-back was able to continue.
Lee Nicholls was looking nervous between the MK Dons sticks and was perhaps lucky to win a free-kick after failing to hold Dion Donohue’s corner.
He then made a hash of dealing with Lowe’s centre and would have been relieved to see no Pompey player nearby to take advantage.
Donohue then tried his luck from 25 yards when Kennedy’s free-kick was only partially cleared, but could not send the ball on target.
With the visitors clinging on, O’Keefe was next to try his luck and Scott Wooton had to fling himself in front of the shot.
And Nicholls then charged from his line to dive on the ball following some fine work between Bennett and Lowe on the right.
MK Dons finally threatened late in the half and it took a fine challenge from Clarke to deny Sow after the striker burst through on goal.
But there was still time for Pompey to double their lead prior to the interval, as a persistent Lowe was able to cut the ball back for HAWKINS to turn home from close range.
MK Dons 0
A Kennedy corner caused issues for the visitors just after the restart, but they were eventually able to scramble the ball clear.
Burgess then had to deal with Gboly Ariyibi’s dangerous low delivery from the right and just about managed to turn it the right side of the post.
MK Dons were looking more of a threat in the second half, but McGee was still a virtual spectator between the sticks.
And Hawkins had a chance to complete a hat-trick on the hour mark, only to swipe at thin air as he tried to convert Kennedy’s cross.
Bennett then missed another decent chance to put the result beyond doubt, firing wide when Lowe’s centre somehow found its way to his feet.
MK Dons might have made the most of that let-off and the Blues survived a couple of nervy scrambles in their box.
Ed Upson then whipped a free-kick into a crowded box and McGee did well to find his way through the bodies and punch clear.
Kennedy received a rousing reception from the Fratton faithful when he made way for Gareth Evans for the closing stages.
And Pompey saw out the final few minutes with relative ease to secure all three points on the sunny south coast.
Pompey (4-2-3-1): McGee; Thompson, Burgess, Clarke, Donohue; Close, O’Keefe (c); Lowe, Bennett, Kennedy (Evans 81); Hawkins
Goals: Hawkins 14, 45+2
Subs not used: Bass, Talbot, Haunstrup, Rose, Oxlade-Chamberlain, Naismith
MK Dons (4-1-4-1): Nicholls; Brittain (Williams 41), Ebanks-Landell, Wootton, Golbourne; Cisse (Agard 66); Ariyibi, Upson, Gilbey (c), Nesbitt (Aneke 46); Sow
Booked: Williams, Nicholls, Ebanks-Landell
Subs not used: Sietsma, Walsh, Lewington, Seager
Referee: Graham Horwood
Attendance: 17,608 (580 away fans)