Berbatov's superior hold up play will likely see him selected in the absence of the suspended Wayne Rooney as a lone striker for Saturday's FA Cup semi-final clash with Manchester City at Wembley.
But Berbatov has regularly been condemned to the bench despite the flying start he had to the season which has him leading the Premier League's goal charts, with 22-year-old newcomer Hernandez preferred next to Rooney in Ferguson's two-striker system.
Berbatov has continued to perform when selected, such as when Ferguson hinted at Saturday's tactics by flanking Berbatov with Nani and Antonio Valencia against Fulham a week earlier, but his season has certainly been undermined by Hernandez's increasing involvement, a fact which Ferguson recognised.
"It is unfortunate for Dimitar because he is a fantastic player,'' said Ferguson of Berbatov's present plight. "But the reasons are obvious. The emergence of Hernandez in the last couple of months has been startling. He is improving all the time and is getting stronger. It is very difficult to leave a player out when he hits that kind of form. Every manager and every player in the country has faced that situation in their career when someone emerges to challenge you. It is the horrible part of being a footballer.''
Signed from Guadalajara as a virtual unknown prior to the World Cup, Hernandez scored his 18th goal of the season in Tuesday's Champions League triumph over Chelsea and has earned comparisons from his manager, not only with United hero Ole Gunnar Solskjaer but England striking legend Gary Lineker.
"I really didn't expect Hernandez to have this impact,'' Ferguson said. "As we said to Ole Gunnar Solskjaer, we thought his first season would be about integration. Solskjaer played in a few reserves games and scored a hat-trick against Leeds. After that (coach) Jim Ryan came to me and said he is a first-team player. We made him a sub the following week against Blackburn and he scored.
"The only advantage for Hernandez was that he'd played in the World Cup so there was a profile attached to him and he had also come from a much tougher domestic competition.''
Two goals in South Africa had indicated Hernandez was going to prove a bargain at £7 million and when he scored a ridiculous goal on his debut in the Community Shield, where he fired the ball into the Chelsea net by smacking the ball into his own face, Hernandez instantly avoided the growing demand for a goal that proved to be Diego Forlan's undoing at United.
Although Hernandez had added six more before the turn of the year, it was his New Year's Day matchwinner at West Brom that really triggered a transformation. That late effort at the Hawthorns was the first in a run of 11 goals in 17 games, six of which he has started on the substitutes' bench.
"Hernandez is fantastic at taking up positions inside the penalty box,'' Ferguson said. "It is natural. He has the instinct to move around and his timing is terrific. There have only been a few top strikers who have had that quality. Ole was one and Gary Lineker probably never scored a good goal in his life, but he was always in space. He'd get rebounds off goalkeepers and was always in really good areas.''
Hernandez's emergence has definitely answered the very public question marks Rooney raised about United's ability to recruit high-class players during his much-publicised contract stand-off last year.
"I don't think he really meant that,'' laughed Ferguson. "I think he was prompted on that one. He probably thought he could make me angry.''