The 44th-ranked, 34-year-old Stepanek beat the 23-year-old Lajovic, world number 117, 6-3, 6-1, 6-1 in an hour and 52 minutes, handing the Czechs an overall 3-2 win.
Lajovic replaced 36th-ranked Janko Tipsarevic, out with a heel injury, while 2010 champions Serbia also missed 76th-ranked Viktor Troicki over a doping ban.
On the hardcourt of the Belgrade Arena, the Czech Republic, playing the third Davis Cup final in five years, scored a ninth straight victory in Davis Cup ties.
Earlier on Sunday, Serbia's world number two Novak Djokovic forced the decisive rubber as he beat seventh-ranked Tomas Berdych 6-4, 7-6 (7/5), 6-2 in two hours and 41 minutes for his 24th victory in a row.
In Friday's singles, Djokovic, the recently-crowned ATP World Tour Finals champion, beat Stepanek 7-5, 6-1, 6-4, and Berdych then saw off Lajovic 6-3, 6-4, 6-3.
On Saturday, Berdych and Stepanek won the 14th of their 15 Davis Cup doubles rubbers together as they swept Ilija Bozoljac and Nenad Zimonjic 6-2, 6-4, 7-6 (7/4).
A year ago, the Czechs beat Spain 3-2 in Prague for their first triumph as an independent country with Stepanek again winning the decisive final rubber.
Former Czechoslovakia, which split into the Czech Republic and Slovakia in 1993, won the cup in 1980.
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ