Despite Merkel's Christian Democratic Union and it's Bavarian allies falling to 37.9 percent from 44.5 percent at the last European election in 2004, they were well ahead of the second-place Social Democrats (SPD), who hit a new record low of 20.8 percent.
"The CDU/CSU alone is stronger than the SPD and the Greens combined," CDU general secretary Ronald Pofalla said in Berlin.
The result mirrored other strong showings from Merkel's partners in the European People's Party (EPP), an umbrella group of centre-right parties in Brussels.
Turnout in staunchly pro-Europe Germany, with votes counted in all 413 constituencies, was in line with continental averages at 42.2 percent, against 42.4 percent five years ago.
The vote in Germany, which provides the largest number of MPs to the European Parliament - 99 - was closely watched for clues ahead of a national vote on September 27 when Merkel is running for a second term.
For the centre-left SPD, junior partners in Merkel's uneasy governing coalition, their score was even slightly down on the 21.5 percent drubbing of 2004, its worst ever result.
Frank-Walter Steinmeier, the SPD chancellor candidate, called the result "disappointing" but predicted that higher turnout would make for a happier outcome for his party when Germany goes to the polls in less than four months.
"Around 42 percent of people voted. At the general election it will be twice that and I will definitely be commenting on quite a different election result," said Steinmeier, also the current vice-chancellor and foreign minister.
The liberal Free Democrats (FDP), Merkel's preferred coalition partners after September, were the biggest winner of Sunday's vote, with their score soaring to 11 percent from 6.1 percent last time.
Together, however, the CDU/CSU fell short of the collective 50 percent they hope to achieve in September.
The Greens reached 12.1 percent, up from 11.9 percent in 2004, while the far-left Die Linke improved their score to 7.5 percent from 6.1 percent.
No other party scored more than the five percent needed to secure seats in the European parliament, including the far-right. In other EU countries like the Netherlands and Austria, anti-EU and extremist parties did well.
Merkel had prepared the ground for a fall in the conservatives' score, saying the situation five years ago was "extraordinary" with SPD chancellor Gerhard Schoeder punished by voters for unpopular economic reforms.
A strident supporter of the EU's reforming Lisbon Treaty, Merkel also said in Sunday paper Bild am Sonntag that it was up to politicians to get voters more interested in European elections.
"In a world with six and a half billion people, 80 million Germans have a better chance of being heard if they can speak as part of a community of 500 million Europeans. Perhaps we have to say this more clearly," she said.
Earlier projections from German public television gave the CDU/CSU 42 seats in the new 736-seat European Parliament, down seven, and the SPD 24, an increase of one.
The FDP would gain four to land on 11, while The Greens and Die Linke both add one to 14 and eight respectively, according to the projections.