Valerien Ismael's side endured a difficult start to the campaign, but are now six games unbeaten and eyeing up the top half after their biggest victory of the season.
Despite just six places separating the two sides heading into the game, the gulf in class was evident throughout as Rajovic's brace and second-half goals for Edo Kayembe, Tom Ince and Matheus Martins proving no more than the hosts' domination deserved.
Injury and illness had forced Ismael into three of five changes made from the goalless draw at Huddersfield, including a first league start this season for goalkeeper Ben Hamer after regular shotstopper Daniel Bachmann was ruled out due to a concussion in training.
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Rotherham manager Matt Taylor opted for a rare two-man frontline in an unsuccessful bid for elusive goals.
Starting the day four points adrift of safety and without a win on the road for more than a year, Rotherham's hopes were dealt a blow after just 10 minutes when Watford scored with their first shot on target.
Ken Sema provided the perfect delivery, whipped from the left flank across the six-yard box, where Rajovic was able to burst through the defence and turn past the helpless Viktor Johansson.
Having offered little attacking threat, the visitors were forced into a change in the 33rd minute when Cafu replaced the injured Sam Clucas. The Portuguese midfielder immediately went closer than any of his team=mates had managed, smashing a 25-yard free-kick with his first touch of the ball which Hamer beat away.
In the fourth minute of first-half stoppage time, the same Watford combination that made the opening goal struck again. Sema outmuscled his defender, turned on the afterburners and squared in almost identical fashion to the opener, with Rajovic tucking home from close range.
Watford added their third in the 54th minute when Ryan Porteous drove at the Rotherham defence and played the ball to Kayembe. The Democratic Republic of the Congo midfielder's expert right-foot control allowed him to turn his marker before firing home with his left.
With all of their substitutes used, Rotherham were forced to play the final 10 minutes a man down after Cafu went off injured, allowing Watford to add two more to the scoreline.
Substitute Ince provided the fourth goal after Ryan Andrews broke rapidly down the right and eluded two Rotherham defenders with his assist.
Martins then wrapped up proceedings in the fourth minute of stoppage time, drilling home after Rhys Healey had turned his defender to work some space on the edge of the Rotherham box.
The managers
Watford's Valerien Ismael:
"We came out of the challenge of losing three games very well. I think now we have built something strong. We need to recover because the next massive block will come in the big December games. But now we feel more ready. We know the players better and what type of players we need for each game. It was a learning process, but we feel we are moving in the right direction. Now the results show up. With the feeling we've had from the beginning that we are on the right path and now the results are showing, it will help to build our confidence.
"The first two goals were exactly what we wanted, to come around the block of the defender. We have to cross more, to shoot more, to force the opponent to defend more, just to keep the pressure on. Today was a team performance because the bench, the players who came in, gave us another breath and got their reward. Another clean sheet and five goals, a great performance."
Rotherham's Matt Taylor:
"It's a painful result, but the end is even more painful. The result is a big blow, but to lose three players of that calibre, for a team like Rotherham, is massive for us. I didn't think there was much in the first half, but the game was past us before we could do anything about it. We've not trained since Tuesday so people can't say we're working them too hard. This league, to a team like Rotherham with our personnel, really highlights our weaknesses.
"We've not been good enough away from home. Last season we ground out enough points for survival. I didn't see enough of that grind and stubbornness today. It's tough at the moment. If you get anything away from home for Rotherham United you've done really well. Our fans can sing and shout whatever they want - I totally understand that because when you're getting beaten every away trip. Why should you spend your hard-earned money to watch us?"